Regeneration

by Rated Ponystar

Rating: teen
Tags: Alternate Universe, Doctor Whooves, Spike, Science Fiction, My Little Pony: A New Generation, Adventure, Violence, Princess Celestia, Crossover, Death, Human, Twilight Sparkle, Lyra, Doctor Who, Gore, My Little Pony: Friendship is Magic, Dark
Length: 100147

The Doctor has to stop the Conversion War and save humanity from Celestia's madness, but a worse evil is playing everyone as pawns for a greater plot

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It's a tale as old as time itself.

A wonderful individual of many faces, a handful of adventurous companions, and a seemingly inconspicuous blue police box.

This time, the Doctor finds himself in a dimension not his own, in familiar lands more alien than the planet he appeared on. Dropped smack dab in the middle of the Conversion War, it's up to him and his new friends to put a end to Celestia's mad ambitions before they can be realized. But the Doctor is no stranger to conflict, and Equestria will learn exactly why he is known as the Oncoming Storm...

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*An Alternate Universe story and crossover with Doctor Who for the Negotations-Verse series. Originally posted in Choice, it was decided to make it its own story after suggestions from readers as well as discussions between me and zelkova48.

Please help out at the Negotations-Verse TV Tropes Page: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Published 2023-01-08 13:30:05 UTC
Last updated 2024-11-16 17:52:48 UTC

Regeneration Part 1

Author's Note

Yup, it's another story to add to the Negotations-Verse series. If you already know about this one, chances are you don't need to read this part. If you haven't, please read. This is an Alternate Universe and Crossover fic for my NegotationsVerse series with Doctor Who. I've always wanted to do a Doctor Whooves fic and when I asked zelkova48, the author of Choice if I could write chapters for them they agreed.

One of those ended up being Regeneration, a popular story in the fic, but as it went forward many believed it should be its own series instead of being part of choice and over time I agreed as well. I talked it over with Zelkova and we agreed to remove the chapters in January and I would start the chapters again as a separate fic. So here we are.

A few things you should know about this before reading it. One, this features an original doctor and not one based on any of the previous Doctors. Second, The Doctor had his adventures (all the canon ones) in the MLP universe and not the Canon Doctor Who universe. Three, I will be making a lot of refrences to the Classic Doctor Who series which is still my favorite over the current one but you'll see them as well.

While eight of the Regeneration Chapters were made before being put down I'm going to repost them once every week instead of all of them in one go.

Thanks for reading and be sure to help out at the Negotations-Verse Page on TV Tropes: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse while also checking all the other Negotations-Verse fics.

Regeneration Part 1

“I’ll be a story in your head. That’s OK. We’re all stories in the end. Just make it a good one, eh? Cause it was, you know. It was the best. The daft old man who stole a magic box and ran away. Did I ever tell you that I stole it? Well, I borrowed it. I was always going to take it back.”

The 11th Doctor

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This was a familiar feeling.

A very familiar one.

He lost track of how many times this had happened in his long life.

Seven? Ten? Thirteen? Twenty-six?

It was almost as bad as how his sixth life ended. Hitting his head as hard as possible on the TARDIS's controls while being blasted by The Rani. Goodness, what an embarrassing way to go. At least Orange Melody hadn't seen it, but that had only left confusion for her when she didn't recognize him in his seventh regeneration at first.

He tried to remember what had happened that caused his TARDIS to act all haywire while the aftereffects of his current regeneration were still sinking in.

First, he remembered who he was: The Doctor. A Time Pony from the planet Gallopfrey, one of the oldest civilizations in the galaxy. Keepers and protectors of time and space.

He was past the year 2,000 in terms of age, and he had managed to regenerate more times than any Time Pony has ever due to a strange mishap that happened in his twelfth life. He had traveled through time and space in his faithful and loving companion known as the TARDIS (Time And Relative Dimension In Space) that could travel to not only alien worlds, but the past, future, and all in-between.

He had fought monsters, alien races, madmen, godlike beings, and even the Loch Ness Monster once. And ever by his side, those who fought with him and helped him along the way were his faithful friends and companions.

They were citizens of Equestria both in the past, present, and future, aliens of different races, and even a robotic dog once or twice. All with different faces, genders, and even races, from ponies to griffins to changelings and more. He had fond memories of many of them but regrets more than one. For they were more than just his friends, they were his family. A family one old stallion in a box would never trade for in his entire near-immortal lifetime.

Speaking of companions, The Doctor then recalled who his latest ones were and what he had just done with them. He, Sunny, and the rest of her friends had stopped the Cyberponies from turning all the pegasi in Zephyr Heights into new weapons for their war machines.

He smiled upon remembering his most recent companions and the first time they met when they both discovered, separately, that ponies were disappearing in the Bridlewood forest thanks to the Vashta Nerada, and they teamed up to stop them. It was clever Izzy who gave him the idea of gathering illumination crystals to create an artificial sun barrier to weaken and destroy them around the areas they had conquered. From there, he offered his TARDIS to them for use and exploration while warning them of the dangers.

After all, more than one companion had died under his watch.

But they all agreed, and the adventures they had were some of his favorites in recent memory. He had said goodbyes to them, needing to check up on something in ancient Equestria, but promised to be back.

The reason for his check-up was when he decided to see how Equestria was doing during the first years of Twilight Sparkle's Alicornation that would eventually lead to her rule. He rarely ever visited that time period in all the years he had been traveling around Equus save for the time he had Silverstream and Gallus as his companions shortly after their second year at the Friendship Academy. Oh, right, he needed to attend their graduation soon. He did promise after they parted upon saving Gallopfrey from the Daleks.

The good thing about being a Time Pony was that you could be there in a flash of a second after not seeing them for about two hundred years. He'd still have to explain the regeneration thing though. That would take time.

Getting up, The Doctor shook his head and cracked his neck. "Well, I still got a head. That's a good sign. Now, let's look at the damage." The good news was that the TARDIS was still in shape. In fact, it strangely didn't look like it had been damaged at all despite all the flare and sparks it was giving a minute ago. "Then again, it could have fixed itself up again. The old girl's done that before. If so, how long was I out?"

He decided to ponder that later. Right now, he wanted to see how he looked. "Well, judging by the voice, I'm male. Again. That's four in a row since the last gender change. Still feel like a pony, but no wings, so that rules out pegasi. I don't feel a magical aura bouncing around in my skull, which rules out unicorn. Earth pony again. I swear I become this more than any other regeneration. I wish I was back in my diamond dog body. That was an interesting experience."

He decided to walk over to the mirror near the TARDIS entrance that he put long ago if something like this happened again. When he arrived, he was pretty interested in what he saw. "Hmm, dark brown mane with an inward shift in the right direction. Still not ginger. Darn. Ash gray-colored coat. Eh, not bad. At least it matches decently with the mane color this time, unlike when I was pure blue with a yellow mane. That didn't look right. The hourglass cutie mark is still there. Eyes are a bit smaller, and that green color? Ehh, I guess it's passable. The nose looks good too. Thank the stars. No freckles or ugly markings. I could honestly pass for a twenty-five-year-old. I swear the older I get, the younger I look more and more in my regenerations."

Clapping his hooves, The Doctor decided to walk over to his TARDIS and check what had happened and where precisely he had landed. "Well, I shouldn't have landed too far from Ponyville. Even if I have a tendency to miss it a lot. We should be about...about...wait, what?"

This couldn't be correct.

These numbers in front of him made no sense because that was impossible.

According to these numbers, which he knew very well, he should be in the middle of a star in the Tralaxia System if his memory of the entire universe coordinates was correct. But that was impossible. He couldn't have missed it by that much.

Deciding to check out what was really going on, he pushed out the TARDIS's sensors and relaxed upon realizing he wasn't in the middle of a star after all, but still in Equestria. Yet, as he looked at the exact coordinate, he paused. This wasn't where Equestria was supposed to be on the planet. In fact, this didn't look like anything from Equus at all. "Has...Has the nation been moved?!"

Now he really needed to get out and find out what was going on.

Practically galloping through the door, The Doctor opened the door and found himself staring into Ponyville just a short distance away. It smelled like Equestria, and the grass tasted like Equestria...but the air was different. No, this was not Equestrian oxygen. Sticking out his tongue, The Doctor calculated what he was tasting and winced. "Ugh, definitely not Equestrian. This is post-industrial revolution pollution type air. That's not supposed to happen for another two centuries! Jeez, how much plastic does this planet have?!"

Shaking his head, if this was not Equus, this was another planet. And if there was industry here, that meant there was another species living on this planet. One that was highly more technologically superior to the ponies of Equestria. This both excited him and unnerved him. It was a mystery that was only getting weirder and weirder. Well, I'm not going to find out what's going on just by standing around.

Rushing back into the TARDIS, The Doctor quickly decided to find the nearest moon he could rest on to get a clear view of the planet while the TARDIS promptly tapped into the communication and networks of the planet. If it was that advance, that is. He soon found a nearby moon about 225,623 miles away and quickly sent the TARDIS there. He felt her land in less than a few seconds and walked out to gasp at the planet. "Oh my..."

It was beautiful.

"Fascinating." Never before since Equus herself had The Doctor seen such a beautiful sight of blue and green. So perfectly mixed together with just the proper formation of continents and landmasses that were evenly split apart for both travel and distance. Waves of oceans as pure blue as sapphires and bright city lights in the distance showed that this was, indeed, an advanced civilization. "Question is, are they hostile or peaceful?"

Were they responsible for bringing Equestria to their planet if it was the former? How would they respond to meeting their new equine neighbors if they were peaceful? Of course, this could also be the work of someone else. A third party that The Doctor either knew or didn't know. I can count at least sixteen different enemies of mine that can do this and have various reasons for it. Although I don't see any starships or planetary defense fortresses. There are just a few space stations that show they are capable of space travel, but nothing beyond their borders. It must be just about discovering atomic energy if they don't use magic. Of course, I could figure out what planet or system this is if...the stars were...wait a minute.

The stars.

He didn't know these stars.

The Doctor had been to nearly every corner of the galaxy, and he knew where every star was. Every consolation, planet, comet, nebula, and more were memories he could recall at any time. And this....this was new. This was not something he had recognized.

A growing dark horror began to feed into The Doctor's heart as he recalled only in specific times when such a thing happened. He rushed into the TARDIS and quickly started doing something he rarely ever did: contact Gallopfrey.

Things might have been much smoother between him and his people, especially after Romana became President, but he still preferred to keep himself as far from his homeworld as possible. He tried the various contact signals, but he got nothing. He then tried the Galactic Federation of United Races's contact signals. Nothing. There was nothing from the Tyroan Empire or the Star Changeling Federation or even space music from the various local alien radio stations.

Nothing but absolute silence.

As if there were no other lifeforms in the entire galaxy.

Save for one.

This one planet where he picked up various broadcasts and focused on one coming from someplace called Britain.

"This is John Smith of B.B.C. news with the latest on the war against Equestria. As viewers know, we recently have entered the second anniversary of the announcement of Princess Celestia's declaration of war for our failures to accept the Magic of Friendship. In reality, our governments discovered her plot to turn humanity into ponies, known as newfoals. This was following the tragic attack on Madrid in Spain, where over sixty thousand people were ponified using the conversion potions, with ten thousand deaths from the attack itself. Reports of an upcoming attack on London proved incorrect as an Equestrian attack force did indeed land on British soil but teleported instead in...Windsor Castle. There are reports of mostly converted humans turned into ponies, but there are casualties...among which... I'm sorry...this is...there are no other words for me to put this. The royal prince and princess, ages two and four, are alive but are now...newfoals. And the rest of the royal family...is gone. Their bodies were respectively given quick deaths...and covered with the flag of our beloved land...All of England and the world is in mourning for these losses...truly...God help us all..."

The Doctor just stood there in silence as he turned to another station. This one is about a battle happening in China where Equestrian forces were turning people in villages into ponies using some kind of potion that The Doctor had never heard before. Speeches in Equestria were being given about how the righteous ponies of Equestria would bring “Light” and “Friendship” to the humans who were misguided and lost in chaos. A blogger on a site called Youtube talking about his best friend turned into a pony and rejected him calling him a sinful human and no longer recognizing him.

There was indeed a force that had been behind this, but it was no alien or extra-dimensional creatures or even cosmic beings. It was Equestria itself.

It had invaded another dimension and was taking over this world.

For once, The Doctor was without words.

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Once he had calmed himself, The Doctor tried to process all that had happened. First, it turned out that Equestria had been on this planet for twelve years, but he had only just arrived recently. According to the computer logs, the TARDIS had to adjust to access a power source to travel in this dimension.

This wasn't the first time he had been in such a situation, so The Doctor made sure to have a few means to make sure his TARDIS never lost her power whenever he traveled to parallel worlds. Once it had converted and adjusted itself, it landed in Equestria just as The Doctor finished his regeneration. It took about ten minutes in the TARDIS, but outside it was twelve years.

The second thing was to figure out who this human species was and how this war began so he could end it. He went into both the human lands and the Equestrian lands to get answers. The former was harder to do, especially since this was a new species hostile to pony-looking life. Thankfully, some ponies kept their morality and sided with the humans though there weren't that many. Even in Equestria, some talk of others disapproving of what was going on could be heard, but they were being silenced.

He went first to a public library and spent an entire day reading the whole history of these people as fast as he could both on books and websites. Overall, The Doctor found them overly emotional and warmongering but clever, creative, and filled with potential to do so much good. They were young. Just starting out as a species despite their faults. No doubt they would have evolved better if Equestria had not come. Overall, he felt he would have liked this species if The Doctor had the time to get to know them, but first he had to save them. Save them from a species he had saved multiple times as well.

That had been the other thing he did right after. Figure out what the blue blazes had happened in the time he had left.

What had caused Princess Celestia, Princess Luna, Princess Cadence, Princess Twilight, and the rest of the Elements of Harmony to suddenly do this mad act without even once thinking of the consequences? He had never interacted with them in his entire lifetime traveling through the timeline of Equestria, but this was not how they were supposed to act.

They were supposed to bring a golden age where Equestria soon created a near worldwide government that would last for hundreds of years before the Darkening Era. Yet, even then, the future would be bright afterward. The Doctor himself had seen it and played a part in it.

They were so critical to the planet's future that practically everything they did were fixed time events.

The Doctor feared even doing the slightest bit of interaction would ruin it all save for meeting Silverstream and Gallus, students at the Academy of Friendship. It had been an accident, one The Doctor would never trade to fix as they had become like family to him, but he had them swear to never reveal what they had done with him to their friends and families or to the Princesses.

The Doctor personally was never a fan of Princess Celestia most of all. She looked every bit of the regal and loving princess that was worshiped by her people, and there was no doubt she was a powerful ruler. But The Doctor knew there was a darkness in her that few could see in the rare times he saw her in passing. One didn't live as long as he did without seeing such things.

Still, nothing she did ever amounted to anything that would overall harm Equestria in the long run save for her death which caused the Crisis of Faith in the Church of Harmony until Princess Twilight dismantled the religion shortly after. Ironically, the atheist herself would convert to the old Fausticorn religion a few years later after her own religious experience.

That is if any of this was going to happen now.

The entire timestream had been completely altered. No, it had been destroyed. Whatever future their old dimension had was no more. That meant anything could have changed. The Doctor's thoughts turned to many companions and friends he knew in the future. We're they lost? Gone forever? Sunny, Izzy, Hitch, Zipp, and Pipp...were they all gone? It was too heartbreaking to even think about.

Yet he knew what happened if timestreams were interrupted, especially at this magnitude.

Had the Princesses been brainwashed into doing this? Forced? Did Discord teleport them? No, even with his power, he was not capable of this. Putting himself into an alternate dimension and maybe an entire town if he tried, but a whole nation of millions? Not possible.

The story, at least to the public, was that Equestria had come over here to teach humanity the magic of friendship, but the consequences led to a powerful energy shield growing from Equestria that was spreading throughout the world. One that was dangerous and deadly for humans to touch.

To spare them from a total wipeout, the Princesses created what was known as the Conversion Potion that would turn humans into ponies. Only after getting his hooves on one of them did The Doctor, and later humanity, realize it did much more.

The potion completely changed not just the DNA of the human, but their mental state, morals, mindset, and even programmed any human touched with it new obedient personalities that were boiled down to "hate everything human" and "love everything pony."

If there was one thing that The Doctor hated, it was when science was used for evil, and this was one of the evilest things he had ever seen to the point that he compared it to a combination of The Master's mind control and The Cyberponies conversion. It was even equivalent to Sutekh’s abilities in some ways. They even sterilize the poor souls, which only made The Doctor vow even harder to find a cure as soon as possible.

It was clear humanity was very reluctant to do this transformation and that their suspicions paid off as it turned out they discovered the same thing the Doctor did. This led to the war. Princess Celestia declared the humans to be unfit for anything but either assimilation or destruction. Calling them pretty much evil but with prettier and sympathetic words as if she had the right to play god over them.

The Doctor had snorted upon that. There were hundreds of more races and creatures far eviler than humanity. Many of which The Doctor had personally dealt with.

He also found out how Equestria managed to get to Earth. They had solved Starswirl the Bearded's Theory of Dimensional Travel and combined it with the power of the Elements of Harmony. The only good thing was they only took Equestria with them. If they had taken the whole planet, the two massive worlds would have collided and destroyed each other.

Which led him to another realization. If Equestria was here...who was raising the sun and moon?

And it was at that moment that The Doctor screamed in his TARDIS so loud that she wept for him.

They were gone.

All of them were gone.

There was nothing left of Equus now but a burned and frozen planet with no life.

That meant that all of his Non-Equestrian friends of the current time and beyond were dead.

Rose. Fizzle The Dragon. Sarah Dane Smith. The Ponds. Gallus. Silverstream.

And so many more.

At that moment, The Doctor would show Equestria why he was known as "The Oncoming Storm."

Because a good stallion was going to war.

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Lyra cursed as she ducked into an alley to escape her pursuers. Ever since she started her public denouncements of Equestria's actions against humanity, her life was in constant danger with little to no aid. Her family had disowned her. Her oldest friends had deserted her. And Bon-Bon? No, it was clear where her views were, even if it hurt to break their friendship.

Worst of all, the Princesses had sent their goon squads to try and capture her. What for, she didn't know, but it couldn't have been anything good. Lyra thought Appleloosa would be a safe place to lie low, but she forgot that "Wanted" posters were a thing, and now she had the local sheriff and his two deputies after him. Plus, it didn't help that she was the only unicorn in an all-earth pony town so she stuck out like a sore hoof. Blasting open the doors of a local barn with her magic, Lyra went inside only to curse upon seeing no back exit.

"There's no point in running anymore, missy!" Lyra turned around as the sheriff and his two goons walked inside with narrow eyes. "Just give up, and we won't have to hog tie ya."

Lyra lit up her horn and gritted her teeth. She wasn't going to get captured here. Not without a fight. I swore to stop this war even if it takes everything from me!

Suddenly, there was a strange buzzing noise followed by a loud snap. Everypony looked up and gasped as a large pile of hay bales fell from the ceiling and landed on Lyra's pursuers. The three were still conscious, but barely as their groans moaned through the pile of hay that had just fallen on them, the rope holding it snapped suspiciously.

Lyra wondered what happened when she felt somepony take her hoof and turn her around. She gasped upon meeting the firm, young-looking (yet his piercing green eyes held such age) mysterious brown-maned and ash gray earth pony as he said only one word. "Run."

Without even thinking, she ran with him outside the barn, past the stunned sheriff and his posse. She then followed her mysterious rescuer out into another alley. He was wearing, of all things, a dark blue admiral trench coat with white lining and buttons while a dark undershirt lay underneath. He looked adventurous in a classic navy commander sort of way but without the fancy medals and decor. They continued to run until they came to the edge of town where awaiting them was some kind of blue box that had "Police" on it. This made her skirt to a halt. "Wait a minute, you're police?!"

"No, I'm The Doctor," He said, reaching the police box and opening it.

"Doctor who?"

"Just The Doctor," He replied. "I think you better get in before they reach us."

Lyra turned around and saw that the sheriff and his deputies had recovered quickly and rushed towards them. She looked back at The Doctor. "How do I know you're not working for them?! Or the Princesses?!"

"Because I'm going to stop them and save the billions of lives on this planet, both human and Equestrian. Before their madness destroys everything good about both races that will last for generations," The Doctor said firmly with such power behind those words that Lyra couldn't help but tremble in fear. "So you have to trust me if you want to save everyone. Because that's what I am offering. A way to stop this."

The Doctor offered his hoof, and Lyra looked at it for two seconds before grabbing it. "Lyra Heartstrings."

"Welcome to TARDIS, Lyra Heartstrings," The Doctor said as he pulled her inside. "And before you ask, yes, it's bigger on the inside than it is on the outside."

Lyra barely had any time to ask what that meant before being dragged into the police box. Almost immediately, it started to make a strange "wooing" sound as it began to slowly dematerialize before the shocked earth ponies eyes. They watched in both fascination and confusion as to the blue box that held the criminal disappeared slowly before any of them could do anything. A minute later and it was gone entirely. Vanished into thin air.

"What...what was that?" One of the deputies asked.

"Some fancy new Canterlot traveling device?" The other said.

"Well, whatever it is, it's gone now. Better send a message to Canterlot about this blue box thing. The Princesses can figure it out, I'm sure."

Little did the sheriff know that the blue box would soon become a nightmare for all four Princesses in the very near future.

Regeneration Part 2

Something has gone wrong. We don't seem to have an archived copy of that chapter.

Regeneration Part 3

"I do what I do because it's right! Because it's decent! And above all, it's kind! It's just that. Just kind."

The 12th Doctor

"The very powerful and the very stupid have one thing in common. They don't alter their views to fit the facts. They alter the facts to fit their views."

The 4th Doctor.

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Princess Celestia could remember when she first had visions about the sun dying.

It was around four hundred or so years ago before her sister returned to her. In her nightmares, the sun was burning red hot like the fires of the underworld. Then it burst into an explosion never seen before in the history of their world.

A sea of hellish flames engulfed the planet as mountains fell, oceans evaporated, buildings crumbled, and ponies screamed in agony before turning to ash. No matter how fast the earth ponies ran, how strong the unicorn cast their shields, or how high the pegasi flew, all succumbed to a fiery death. The flames would spread throughout the world and leave nothing more than a dead husk floating in space forevermore.

When it was over, Celestia woke up screaming in horror, and it took hours to get her guards to stand down upon thinking she had been attacked in her sleep.

At first, she had thought it was simply a bad dream. But then she kept having the same one, again and again, each and every night to the point where she suffered from lack of sleep for hundreds of years.

The power of dreams was something that Celestia was no expert in. That was her sister's department of arcane knowledge, but she did know that "a recurring nightmare could be perceived as an ill-omen. A vision was all too clear to her: The sun would die and take all life with it.

Knowing that time was against them, Princess Celestia spent hundreds of years trying to save their world, but all she could do was protect her ponies.

Equestria would avoid the doomed fate of all the other nations even if, deep down, Celestia felt utterly guilty for doing so.

Princess Celestia was no fan of outsiders, pony or non-pony. The years of having to defend her home from countless invasions were enough to make her distrustful of them unless they fully embraced Equestrian society and their way of life. She had hoped to change the world with the powers of Friendship and Harmony so that all embraced their culture.

Alas, it was not meant to be.

She asked no forgiveness for what she had done because she knew there would be none to give.

The night they arrived on Earth for the first time, she drank herself to a stupor and cried all night in private with silencing spells around her. If she believed in such things as afterlives, Celestia would have declared herself doomed to Tartarus upon her death. But she had to be strong for her ponies and the future she hoped to bring to them.

Celestia sacrificed her soul and morality to save them from utter destruction. The least she could do for her subjects was give them a golden future where there would be no threats, no evil, and no sin. They would build a new one from the ashes of the old world that would achieve great wonders long after Celestia passed on.

The only problem was humanity.

A race of nothing but savages who embodied the worst of cultures and beliefs centered around hatred, selfishness, and bigotry. Princess Celestia quickly developed a mix of pity, loathing, and disgust for this species that should have destroyed itself long ago.

Still, they survived regardless while learning nothing in her eyes. Losing her adopted daughter, her beloved Sunset Shimmer, to them only worsened her opinion of them.

Soon her nightmares were filled with images of humans coming into Equestria, taking it over, raping her lands and her people, and treating them like animals while Celestia wept at the graves of those she loved. She would not let her subjects suffer at the hands of these monkeys. She would die first.

The visions had to be correct, after all. They were right about the sun. Why not be right about humanity? And so she did what she could to save them, even if they didn't want it, but in the end, the war had come. But she believed they could win. Even if it took time, the humans would submit to them thanks to the potion, the barrier, and their way of life.

And then she learned about The Doctor.

And her nightmares soon had his face in them.

Princess Celestia called for an emergency war council meeting as soon as Discord was done talking and told them of their new enemy. Of course, she had to say a few lies, but they believed he was a threat in the end.

Even if some were skeptical, an alien who had caused massive suffering and death in Equestrian history was enough to frighten them. Naturally, they had to keep a lid on his true identity to prevent an outright panic and simply said he was a terrorist in league with Equestria's Most Wanted Pony: Lyra Heartstrings, which wasn't far from the truth.

For over two months, Celestia and her allies waited to hear any sign or appearance of The Doctor or Lyra, but there was nothing. This only unnerved her even more. That didn't mean she wasn't facing problems, however.

The non-ponies in Equestria had gotten more riled up. They were nearly revolting out of fear of being made into ponies against their will like the humans. Something that Celestia was uncertain about doing or not since the non-ponies in her land always assimilated very well, but apparently, there was a limit.

Seeing them perform acts of riots and violence had made up her mind, and she forced them into internment camps for now. The Conversion Potion was only capable of turning humans into ponies, but with some tweaks, perhaps it could affect other races as well.

This move caused groups of ponies, especially friends and spouses, to speak out against this action. Luna then thought of creating a task force to prevent further uprisings or discontent, so they started the Equestrian Secret Services.

They were authorized to ensure that Harmony was kept in place and that citizens were devoted to their noble cause. To make sure that there were no rebels or traitors who were thinking of causing problems or escaping to the human side. However, this didn't seem to fully work as there were reports of numerous ponies attempting to leave Equestria to the point that an "Underground Railroad" had been established to help them escape. She quickly made it law that anyone trying to use this "railroad" or being part of it would face prison.

Second, the U.N. had accused Princess Celestia and Luna of genocide against the species back home by accusing them of letting the sun and moon motionless in the air. According to anonymous sources, they stated that their home dimension was dead due to nobody being able to move the sun and moon without the princesses there.

Naturally, Equestria was divided about whether or not this was true, but Princess Celestia had reacted as fast as possible to hide the truth. Princess Celestia quickly put out a public statement across the nation saying that it was a lie and that she had left a plan for their allies in Saddle Arabia.

Long ago, Celestia and Luna created an amulet that was designed to hold both their powers and could be used to make sure the day and night cycle continued. It was this object she left behind for the Arabian royals to use to make sure the world continued its celestial process.

Of course, this wasn't the truth. It had never been completed due to Luna being on the moon before it was fixed, and she had lied, saying she had finished it in the thousand years she had been gone.

Regardless, most of the population, including her own sister, Twilight, Cadence, and their friends, accepted this, but ponies still doubted it. And doubt was enough to unravel things, so she quickly began making harsher rules in censorship and quickly centralized all news media to the crown. She had no idea who was behind figuring out the truth and leaking it to the world, but Celestia was willing to be The Doctor, or Discord was behind it.

Which led to the worst problem of them all. Like Discord promised, he had gone to Fluttershy and gotten her out. He went to all of the Elements, and even Spike himself, to convince them to leave in fear of The Doctor. They all refused for various reasons, but Fluttershy went with him. The others had been horrified and thought maybe she was brainwashed, discorded, or taken against her will. Nopony had seen them or the Element of Kindness since those two months...until now.

"Are you sure of this?" Princess Celestia asked, doing her best to hide her tone of disappointment and anger. Princess Luna, on her throne, looked both shocked and livid as Agent Bon-Bon of the ESS bowed before them.

"I'm sorry, your majesties, but the prisoner confirmed it," Bon-Bon said stoically, yet her stance was filled with anger. "Fluttershy and Discord are part of the Underground Railroad to get ponies who want out of Equestria and into the human lands. They've been working together with the U.N. in doing so."

Celestia tore the paper in two with her magic. How dare she?!How dare Fluttershy do this to them? To work with the enemy? The humans? Discord wasn't a surprise due to his chaotic spirit, and he had betrayed them already with the whole Tirek debacle. She really wished she had just turned him to stone or executed him after that, but the girls had insisted on giving him another chance. But Fluttershy?! Why?! I know she didn't like this war, but to outright defy us and work with the enemy?

"Have Princess Twilight, Princess Cadence, and the others been informed?" Luna asked sternly.

"They have...they didn't take it well," Agent Bon-Bon replied with a heavy sigh. "Our information says they're making their way with another group of escapees to Osaka, Japan. Princess Twilight is very determined to stop them and has decided to go through with the attack earlier than planned with Commander-General Shining Armor and Princess Cadence. They should be starting tomorrow."

"What are we going to do, Sister?" Princess Luna asked.

Princess Celestia sighed and closed her eyes. Much as she was angry, she needed Fluttershy alive. She was the wielder of the Element of Harmony, and she needed every weapon Equestria had not just for humanity but for whatever The Doctor was planning. Besides, there are memory spells we can use to make her forget her rebellion. We can always just say Discord manipulated her.

"Fluttershy is to be captured at all costs. Discord is to be eliminated. Tell Twilight she has full permission to use whatever means she wishes in the attack," Princess Celestia ordered as she held her hoof out. "Make an example of this one. I want as many newfoals filling up Osaka that they'll be swimming in it."

"Yes, your majesty!"

+}{+

It would shock anyone who knew the Spirit of Chaos to learn that he hated war. Having seen his planet's entire population reduced to just himself would be enough to drive anyone to hate killing.

In all honesty, the death of his entire race had affected Discord more than he liked to admit, but could anyone blame him? Seeing your entire culture, planet, family, and friends "exterminated" by cold and vicious machine-like abominations that had developed the means to negate your reality-warping powers would change anyone.

It didn't help that the natives of this world rejected and feared him because of his alien appearance. So yes, he went mad. He went crazy. But deep inside, he was just hurting and crying because he was still processing it all.

He wanted to just let it all out and rage against this perfect planet that had never known true horror and destruction like he did. A place that was supposed to be a new home his parents sacrificed everything to send him to but rejected him out of fear. Even after holding the entire world at his mercy, Discord did not feel any satisfaction deep inside. Only a hole that couldn't heal and a wish that he never left home in the first place.

Even if it meant joining his people in utter destruction.

After meeting Fluttershy, Discord finally began to wake up from his inner nightmare. She was the first, the very first, pony to get him to open up, but he was hesitant. A trick. Deep down, he believed they would reject him again because of who he was and that he would never be one of them.

He joined Tirek because he thought it was inevitable, but it hurt doing so, and he didn't know why. Only after he lost his powers and was at Tirek's mercy did he understand how low he had fallen and what he lost a second time. Twilight sacrificing her magic for even him had opened his eyes and accepted the truth. He had to change. Be better. And opened up again to others. Because there was no other way to heal what he had lost.

The day after nearly losing everything a second time with his betrayal to Tirek, he confessed everything to Fluttershy. Losing himself in tears and anger, he told her his true story: where he had come from, what he had seen that day, and what he wished deep down. At the end of it all, Fluttershy wrapped her arms and wings around him and let him sob endlessly on her shoulder while crying beside him.

She told him that he wasn't alone anymore and that she would always be there beside him. He promised to be good this time. Not just for his sake but for Fluttershy, who had put so much faith and determination to help him. All he really needed to help wound his damaged heart was just a little kindness.

This is why he got Fluttershy out of Equestria as fast as possible, despite her hesitation. He had begged her to trust him, just this one time to believe him when he said that danger was coming. He knew of The Doctor.

The whole universe knew of him.

The Time Pony who was like fire and ice. The storm that knew no end. A being that made angels cry with joy and demons shiver in fear. If he was facing Princess Celestia as an enemy, she must have done something terrible. Fluttershy listened, thought long and hard, and agreed to go with him in the end. The same couldn't be said for her friends.

Discord tried really hard to get them to understand. He begged, pleaded, and promised as well as he could that he was trying to help him, but the results were poor.

Twilight believed too much in her mentor to think she had done something terrible. Rainbow Dash and Applejack were full-on believers of the war, and they accused him of being a traitor quickly. Rarity didn't like the war, despite her husband fighting in it, but she didn't trust Discord and probably never had. Pinkie Pie refused to leave because she didn't want to leave behind her friends and family but secretly wished him good luck. He tried his hardest with Spike, who admitted he hated the war and everything going on but wouldn't abandon Twilight.

In the end, he only took Fluttershy, her animals, and her cottage and teleported them to an isolated place in Yellowstone Park with a spell or two to hide them from everyone. And then, two weeks later, the U.N. put up their statement about what had happened to Equus. Discord knew what Celestia had done in that instant, and Fluttershy cried for five days straight.

Once again, Discord had lost a home.

When they arrived on Earth, Discord knew that there was something else planned besides trying to help humanity. He knew Princess Celestia better than she knew herself. She was not the perfect goddess she portrayed herself to be, but bitter and racked with inner rage, much like himself.

He wondered what she experienced as a child to make her who she was but decided it was probably useless to figure it out. Especially when it was all clear when the statement about what had happened in their old world came to light. Naturally, Princess Celestia denied it, and most of Equestria believed her, but some figured out the truth and rejected her.

Fluttershy demanded they help them. If only to give them a chance for a new life. Discord hesitated until Fluttershy pointed out that what was happening to humanity was what happened to Discord's people. They were not just being exterminated. They were being converted and dying inside while living as nothing more than automatic dolls. Soulless machines who did whatever Celestia programmed them to do.

That had won Discord over in an instant.

He would not allow what happened between his people and the Daleks to happen again. Even if it was not his people, his home, or even the same enemy, he wouldn't let this happen again. Which was why he was doing everything he could to protect Osaka from Equestrian forces.

They were really going all out on this one. Firing magical-based artillery and mega spells from the unicorn lines while protected by a giant magical shield protecting their central teleporting zone and any territory they picked up.

Pegasi were dive-bombing in the air and taking out any high-ranking targets with strategical strikes or unleashing bombardments of the potion to cause confusion in the ranks. And every street had armies of earth ponies charging forward with magical armor and gear, stomping on any threat against them.

Already they had all of the southern sides of Osaka from Nishiyodogawa to Higashisumiyoshi, while the humans were holding out on the northern side from Yodogawa to Hirano, with some of the fiercest fighting being in Kita, Chūō, and Tennōji. The last one was where Discord was personally.

It was a clever move as well.

Most of the U.N. forces worldwide were spread thin, trying to save what lives they could from the growing barrier while dealing with multiple attacks in Europe and South-East Asia. While the JSDF was doing what they could with what the U.N could spare, most of their best forces were in Kyoto and Tokyo at the moment and would take hours to arrive.

He knew why they were here. Fluttershy and Discord had arrived with their latest group of escaped ponies with a few other members of the Underground Railroad. Osaka was their last checkpoint before crossing over to the United States. Then the attack came, and Discord had to put his energy into protecting Osaka as much as possible while Fluttershy fled with their group.

Already their numbers had dwindled in the opening attack, and he was doing what he could to give Fluttershy enough time to get to the U.N. forces.

Snapping his fingers left and right, Discord unleashed as much chaos as he could: storms sending down lighting that turned ponies into chickens, giant samurai statues coming to life to hold off the enemy, summoning living anime characters to fight against their invaders, and turning weapons into sashimi. All while teleporting ammunition, soldiers, and wounded humans in and out of the battle whenever he could.

But Equestria kept coming, and Discord was spread thin. His powers were weaker in this dimension, and he couldn't do as much as he used to back home.

Discord was about to fly a bit higher when he felt a blast of magical energy nearly rip his horn off. He ducked down and flew close to the ground. Preparing himself, he grumbled upon seeing two familiar figures fly down while another rushed towards him with a squad of Crystal Pony Soldiers in their best diamond armor and weaponry.

Seeing Twilight Sparkle, the ever-living bookworm, dressed in gold and purple armor while holding a long amethyst glowing crystal sword was still amusing. While Princess Cadence wearing platinum armor mixed with different crystals was also funny to see due to being the princess of "love" and all. Especially since she had two bloody crystal axes in her magical aura. Prince-Consort Shining Armor, dressed in his usual purple armor, was the only one who looked the part of all three members of the Sparkle family.

Holding the Commander's Sword given to him by Princess Celestia at the start of the war, Shining Armor shouted, "Discord! In the name of the Princesses of Equestria, you are to surrender for your treason! Again!"

"Funny," Discord said with an amused smirk. "It's ironic that I'm being declared a traitor when your own Princess Fatsun is the one who betrayed our world."

"Those are just lies, Discord! Lies that you no doubt spread to cause chaos in Equestria!" Twilight shouted as she landed on the ground next to her brother, seething with rage.

"Believe it or not, Twilight, I didn't do such a thing, but I really should have realized it when I learned that The Doctor is here," Discord said with a shiver. "No wonder he's fighting against Celestia. To have her ruin the world that he once cared for so much and saved multiple times? Quite frankly, I hate to see what he has planned."

"Again with this "Doctor" pony," Cadence said with an eye-roll. "I am willing to believe my aunt's statement's about him being dangerous, but since we haven't seen him in two months, I'm willing to believe he doesn't even exist. Just another lie by you to scare us."

"Trust me, Cadence. I am a liar, I will admit that, but when it comes to The Doctor? I tell nothing but the truth," Discord stated as he glared at them. "And the truth is you are all being played by Celestia, who doomed everyone else back home. You've been manipulated into thinking you are doing a great crusade to save an entire race when you are practically genociding them and their culture. I always knew you ponies were selfish, arrogant, and self-righteous to the point of narrow-mindedness, but I never believed you were also stupid. Especially you, Twilight!"

He pointed at her and glared. "I respected you greatly for beating me. You were smart and clever to outwit me, and I saw you as a worthy adversary and later a friend. I practically thought of you as one of my closest friends after you saved me from Tirek despite all I had done. But what I admired most was that you were so faithful to the ideals you preached throughout all the time I got to know you about friendship. Well, I guess the truth is you're nothing but a hypocrite along with the rest of your friends except for Fluttershy. What makes you different from the rest of the ponies of Ponyville, who feared and hated Zecora when she came to town? What makes you different from Starlight Glimmer, who forced ponies to give up their cutie mark for equality and greater good? How are you different from Queen Chrysalis taking over Equestria against their will?"

Twilight was about to say something, but Discord wouldn't let her do so and instead turned to Cadence and Shining Armor with a snort. "And you two? Princess of Love, my scaly butt. You outright condemned the romantic relationships between humans and ponies. Do you know how many ponies I've helped leave Equestria so they could find the humans they loved? How happy are they together? And those you deny and capture suffer heartache while between bars. Did you once tell me that not all nobility accepted your relationship with Shining Armor? Well, I guess now you know how they felt about you two."

He then turned to a snarling Commander-General. "Meanwhile, Shining Armor here is being used as his tool. Instead of thinking for himself and fighting for justice, he's being used to promote a hostile takeover of a nation and eliminating the people on it like a good little soldier. You know that feeling you had when you were brainwashed by Chystalis during your wedding, Shiny? That's what the newfoals deal with every day, thanks to your potion. Your daughter should be ashamed of you!"

"That's enough!" Shining Armor shouted as he stomped his hoof so hard on the concrete street that it cracked. "What right do you have to preach about anything?! You're chaos incarnate! You drove ponies insane in some twisted sense of humor! You took over our land! Corrupted our subjects! Turned us against one another! And betrayed us to an enemy who nearly destroyed everything we built only to do it again even after giving you another chance! You are a selfish, immature monster who should have been smashed as a statue or dropped into a volcano!"

Discord stared at the ponies, who glared at him with utter hatred and sighed. "You are right. I am a monster. I never realized it until after Tirek, but I was no different from those that ruined my life, so I ruined others to deal with that pain. I went through a tragic moment in my life when I lost my people, but it doesn't excuse the actions I took to deal with it. Discording ponies really is no different from turning humans into newfoals." He narrowed his eyes and pointed to them. "Yet, you ponies showed me there was another way. Another means to help me. Friendship was what saved me, and Fluttershy is everything to me because she taught me to really laugh, smile, and love. I took it all for granted until I was betrayed by Tirek. I swore to use it well when you all gave me another chance. Believe it or not, I saw you as my friends despite everything we went through."

He then snapped his fingers and found himself dressed in a familiar green tunic costume with a copy of The Master Sword and Hylian Shield from a game he played not long after their arrival here. "But you know what the difference between you and me is? I at least admit that I was wrong, and I'm willing to admit it now. You, however, are not. I'm protecting humanity not just because Fluttershy asked me to, but because it's right. I saw one world burn to ashes with a race of evil beings destroying everything good about it." He then pointed the sword at them all. "I will not allow it to happen again."

"...Tell us where Fluttershy is, Discord," Twilight said while raising her own weapon. "And we'll make sure you are put in stone instead of outright execution."

"You want her? You have to go through me," Discord said as there was a split second, and both sides charged at each other.

+}{+

"You know, I never really understood Eco-terrorism," The Doctor said as he used his Sonic Screwdriver to work the controls of the nuclear power planet to cool it down. He had decided to make a new one after using the last of his old one to save Lyra, and the TARDIS was quick to give him a spare. The baseline was made out of a special near unbreakable crystal that allowed the glowing swirls of energy mechanics to be noticed. At the same time, the white orb on the top continued to glow in whatever color he needed. It had a black and white handle with white Gallopfrian language that had meant "The Doctor" on it so people would know who it belonged to if it was lost. Although, in hindsight, very few knew the language.

"I mean, I do understand the reasoning. Wanting to save the planet from utter pollution and ecological destruction is a nice thought, but the way so many races go about it is stupid. Blowing up buildings, killing people, setting fire to everything, and blowing up nuclear reactors?" He snorted. "You realize that radiation is deadly and spreads around, affecting flora and fauna, right? I mean, the city has a zoo and reservation section nearby. And you were talking about saving the plants and animals while doing this?"

A few humans in muffled voices said something in the back, but The Doctor shrugged. "Well, it wasn't a full-on stupid plan. Infiltrate the staff, find out the codes and details of the workings, bring in a few guns and open the door to storm the place. Then cause a meltdown to make it look like things went wrong instead of outright sabotage. The stupid part was bragging about it on that one site. Reddit, I believe?"

Another few muffles were heard as The Doctor finished shutting the power planet down and put his Sonic Screwdriver away. Walking over to the tied-up and gagged humans, he glared down at them. "Well, good thing that your little plan failed. I also managed to hack your computer systems at your base, found all the locations of your fellow terrorists, sent the data to the police, and they should be coming here in about ten minutes. Quite frankly, I should be shocked that there are radical humans like you who think that humanity needs to be turned into ponies out of your own personal misanthropy, so you decide to cause as much damage to your own people as possible. But I'm not. I think I'm just getting numb to things like this at my age."

The sound of feet rushing down the hall, followed by hooves, alerted The Doctor, who turned around and saw a lip bleeding and blackened eye human dressed in a tactical armor growl upon seeing The Doctor and charged at him. A few seconds later, a worried-looking Lyra followed and shouted, "Doctor! Look out!"

The Doctor calmly waited until the human was close enough to shift to the right to avoid his punch and swiftly brought his rear left leg to his gut. "HAI!" The blow to the solar plexus caused the terrorist to go down on their knees, where The Doctor cried out again and delivered a downward chop to the back of the neck. Dusting his hoof, The Doctor smiled. "Venusian Aikido. Good to see I still remember the basics."

Lyra rushed over and looked at the console. "The reactor?"

"Silent as a sleeping baby," The Doctor said as he took out a pocket watch from his coat. "Police should be here in two minutes. Tie him up, Lyra. Let's get going."

Lyra nodded and used her magic to tie up the unconscious terrorist before kicking him in the face for good measure. Following The Doctor, Lyra then asked, "Doctor, forgive me for saying this, but shouldn't we be doing more?"

"What do you mean?" The Doctor asked as he continued onward without looking back.

"Well, it's not that we haven't done a lot," Lyra said as she pointed out all the things she had done with The Doctor since her rescue. "Using the TARDIS to go back and forth to help ponies escape Equestria. Exposing the truth to everyone worldwide about what happened to Equus, even if Celestia did massive damage control. Using the TARDIS to warn areas of attacks ahead of time to better prepare the humans. Not to mention shutting down groups of fanatics like these who want to destroy humanity and turn themselves into ponies because they believe it is the best way to save their species and the planet."

"Don't forget how we prevented that crazy Turkish general from blowing up Istanbul with a nuclear weapon because three-fourths of the population got ponified," The Doctor pointed out as he used his key to open the TARDIS.

Even though she had been inside the strange blue box multiple times in the past two months, Lyra was still amazed by it every single time.

The main control center was sleekly clean, with numerous buttons, switches, and gizmos that she didn't know she could do. There were also giant blue screens with various symbols that she didn't recognize, but the Doctor did and only assumed they were in some kind of alien language. The center crystal tower was the most beautiful part as it glowed like a rainbow and with rings going up and down each time it was used, while computer screens attached to its base could be moved around for usage.

The interior was a mixture of white and tan with glowing white circle lights that she asked about, but The Doctor confessed he didn't know what those were for. The floor around the TARDIS was made of class with two sets of stairs leading to the control center's platform encased in steel golden with silver railings and comfy black leather seats for sitting down by the edges.

To the left of the TARDIS's mainframe was a giant computer with multiple screens recording information about the war from the U.N.'s HQ or showing various news reports of the war itself. There was even a tactical map in the center showing the entire world with positions of various military forces for both sides of the war. To the right, there was a set of Victorian-style oak chairs with a large tea table with warm tea prepared and biscuits, scones, and crumpets on a plate that read "To Doctor, From Yaz." A series of books were on the shelves around it, along with an old telephone that actually worked surprisingly.

The Doctor said one needed to rest and relax in times of war so that you didn't get burned out. Lyra still hadn't figured out it managed to automatically fill itself up with different tea each time or where the goodies came from. And finally, in the center was the giant hallway that led to other parts of the TARDIS, including the bedrooms, bathrooms, laundry room, clothing room, garden, pool, billiard room, weapons department, laboratories, and more. According to The Doctor, he had only explored fifty-nine percent of the TARDIS, and he didn't know what else was inside her.

The Doctor walked over to the console and activated the TARDIS, sending her off through the waves of time and space while he began to check something on one of the computer screens nearby. "I'm guessing you think we need to do something more? Don't worry. I have plans to do so. We're just waiting for the right moment."

"You have a time machine," Lyra pointed out, shaking her head in confusion. "Can't we just use that to go to the right moment in the future or go back to the past and prevent the war from happening at all?"

"Unfortunately, no," The Doctor explained with a heavy sigh. "Time travel is complicated. It would take three of your lifetimes to explain even the basics. For one, this dimension operates under a different set of laws regarding time, much like how physics is different here than back home. Second, going too far into the future could prevent us from missing something important. The most I'm using the TARDIS for is to go into the future for a few days here and there. And changing the past has consequences with only the most extreme reasoning needed to do it. I did go back to when Equestria first landed, only to find out that we're now a fixed time event. Meaning that we cannot change this or the entire history of his planet will alter, and what happens afterward could tear everything apart for the worse."

Lyra slowly nodded her head and decided to trust his reasoning. After all, he was the expert when it came to this. She decided to walk over and noticed he was concentrating on a set of numbers and chemical formulas that made her tilt her head. "What are you working on?"

"A cure for the Conversion Potion," The Doctor simply said.

"What?!" Lyra shouted in shock. "How long have you been working on a cure?!"

"Since I learned about it," The Doctor said before pausing and looking over the data while rubbing his hoof to his chin. "It's actually very advanced for the magic and technology Equestria has in its period. I've seen similar alchemic and mathematical formulas before, but Twilight really outdid herself this time. Too bad it's being made to be used for evil. There are numerous ways this can benefit physical and mental health."

"How close are you to a cure?" Lyra asked, eager to see the look on Equestria's face when their prized newfoals turned back into humans.

"Oh, I created one about two weeks after I started," The Doctor said before shaking his head. "The problem is that it's designed for one specific newfoal and no other."

"What do you mean? A cure is a cure, right?" Lyra asked as The Doctor pressed a few buttons, and a hologram shot out of the TARDIS showing a pony, his DNA, and what looked like more chemical data.

"The problem is that the potion has a unique enzyme that comes from Celestia's own blood. It's been used to create the central chemical compound for the potion," The Doctor explained. "What the enzyme does is find a unique portion in the human DNA that allows it to modify the human into any of the three pony races based on the information it gathers from the strains. This unique base is always different for every human, but it forms the basic building block for the new DNA that replaces the old one. Because of this, every cure would either need to be different. That would take a long time. Fortunately, there is an alternate solution. I need a counter enzyme that is the opposite of Celestia's blood to neutralize this."

"Any idea where we can find that enzyme?" Lyra asked as many lights began blaring from the "War Computer" that made the Doctor rush towards with a smile on his face. Lyra soon followed and watched as he typed into the computer with haste. "What is it?"

"The enzyme," The Doctor said as he pulled up a screen that showed shaky footage of what appeared to be Discord dodging giant missile-like spells from Twilight and Cadence while summoning a big umbrella to bat them away. "Discord's blood is the key. If I can get a small sample of it, I can have a cure that will affect every newfoal regardless of their differences. Plus, where Discord is, Fluttershy is there to follow, and we need her for the next part of my plan."

Rushing back to the TARDIS main controls, The Doctor knelt down and opened a compartment with junk inside it. He started digging through it while licking his chops as Lyra walked over. "Let's see..." He popped up and held a recorder in his hooves before giving a nostalgic smile. "Huh, I was wondering where that was." He played it a few times before handing it over to Lyra. "Maybe in here?" Rising back up, he looked at a giant green crystal ball with screaming voices. "Nope. Not it." He handed it also to Lyra, who rolled her eyes before he dragged out a very long scarf, and raised his eyebrow. "Ugh, why does this always appear every time I regenerate? It was a fun time, but I've outgrown it." He tossed it over his shoulder, where it landed on Lyra's head. She puffed it out of her eyes just as The Doctor shouted in triumph and pulled out what he was looking for. "Eureka!"

Lyra, levitating the other stuff away, asked, "What is that?"

The Doctor presented it to her. It looked like an amulet of sorts with six jewels circling around what appeared to be miniature radar. The jewels were in the colors purple, green, blue, red, yellow, and pink.

"A surprise," The Doctor said as he rushed over to the TARDIS and started putting in controls. "Alright, the next stop is Osaka! We will find Discord, get Fluttershy, stop the battle, and save Japan! Next stop, the human base of operations in the city! Tally ho!"

Pulling the lever, the TARDIS moved and jerked around for a few seconds before stopping. Smirking, The Doctor put the amulet in his coat pocket and walked towards the entrance. "Well, let's go."

"Where are we? In the base?" Lyra asked.

"Don't be silly," The Doctor said with a smile as he put his hoof on the doorway entrance. "We'd freak everyone out if we did that. No, I landed us a few feet away so we could calmly walk over to the guards and explain that we are here to help. I've been traveling for about two thousand plus years in the TARDIS. I know how to manage her."

Opening the door, The Doctor soon found at least half a dozen barrels of assault rifles held by UN soldiers aiming at his face. He noticed that he was not outside the military base like he had planned but instead seemed to be in the center of communications, where everyone inside was staring at him with fear and confusion save for the guard holding him. The Doctor turned to Lyra and said, "Of course, sometimes, there are margins of error."

Lyra couldn't help but facehoof.

Author's Note

And here we go with part 3. Be sure to help out at the TV Tropes Pages for the Negotations_verse series: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 4

“There’s always something to look at if you open your eyes!”

the 5th Doctor

“Lives change worlds. People can save planets or wreck them. That’s the choice. Be the best of humanity.”

The 13th Doctor

+}{+

If there was one thing that Major-General Marshall Highmoor knew when he joined the military, it was that war was coming.

Having come from a family of soldiers that had fought for his home country of the U.K, he signed up for the army right out of school not just because of tradition but because the world's tensions were leading to another world war.

The 2020s were, for lack of a better word, fucked up.

Political corruption, economic recessions, tensions between superpowers, climate change officially declared irreversible, resources being hoarded up, and even revolts in various first and third-world countries that had to be put down in bloody fashion. It's a miracle that things didn't escalate into a world war then, but the actions and consequences brought everything to the powder keg that was the 2030s.

And then aliens from another dimension came, and everything changed.

No longer did mankind have to only worry about itself, but now multi-colored ponies with magic had become the greatest threat to humanity since the near start of nuclear conflict during the Cuban Missile Crisis.

Marshall Highmoor had no personal prejudice against the Equestrians. Some of them he got to know very well since his sister was an ambassador for the U.N. However, he never trusted the Equestrian government's statement that they were here for peaceful purposes.

A peaceful nation doesn't come here with an expansive shield that is deadly for all but their own kind to the touch. A peaceful nation doesn't put bans on certain contrabands that are harmless in the name of "cultural appropriation." And a peaceful nation doesn't create a means to turn you into a different creature without your original personality.

No, Equestria came as invaders, and the war now was only proving it.

Knowing he would be needed, Marshall Highmoor left his majesty's forces and joined the U.N. forces, which had grown powerful since its founding due to alien existence being a thing. No longer was it a peacekeeping force but a full-on armed military that spanned the global nations of the world.

However, when you were fighting enemies that could teleport anywhere, manipulate weather, defy the laws of physics, and fight with the strength of two or three full-grown men, numbers could only do so much.

He was doing what he could to hold onto an important city in Japan while the Equestrians were throwing everything at them. He knew why they were here. He had been in contact with Underground Railroad members Fluttershy and Discord, who had become allies to humanity upon the revelation of their old world's fate.

Major-General Highmoor never thought he'd live to see the day when he would be fighting a foe more evil and sinister than Hitler, Pol Pot, Mao, or Stalin. But to let your entire world burn to take over another one? Hell awaited Celestia for sure.

Only now, Hell had come to Osaka with half the city under the control of the invading Equestrian force while the other half was still in his hands. Reinforcements were still at least two hours away, and the Equestrians were converting every human they could while killing those who resisted out of rage and anger. They were primarily driven to capture or kill their two biggest traitors.

"How's Discord doing? Any word on Fluttershy's group?" the Major-General asked as he walked beside one of the few equine U.N. soldiers that had joined humanity's side. The pony, Private First Class White Chalk, was white coated with a dark black mane that he buzzcut when joining the military. Not all equines had agreed with Celestia, and there were a number of them all over the world, helping humanity in whatever ways they could.

The private soon answered. "Discord's doing his best with Princess Twilight, Princess Cadence, and Prince Shining Armor, but he's already wasted so much of his powers helping us that he's already starting to tire out. As for Fluttershy and her group of refugees? They are still behind enemy lines, and we have no idea where."

Marshall Highmoor rubbed his forehead. "Great, and now we got two spies to worry about."

"Um, about that, sir," Private White Chalk stopped and looked serious at his superior officer. "The mare that we captured said her name was Lyra Heartstrings. I took a look at her and asked a few of our other pony soldiers. We've all identified that it is, indeed, her."

"She was the most vocal pony against the war, right? The one who wrote that book about her visits to our lands and advocated for cooperation?" Major-General Highmoor asked, rubbing his chin. He recalled hearing his troops about her a few times from the grapevine.

"Yes, sir," Private Whitechalk said before shrugging. "Unless she is a changeling, which I doubt, I think she's the real one. The other one, calling himself The Doctor, is unknown to us, but Lyra says they're here to help us."

"Hmm, we'll see," Major-General Highmoor said as he continued to the interrogation room. According to witnesses, a blue police box materialized inside the base, and both this "Doctor" and Lyra exited out of it. They could not get any readings off the box, nor could they enter it, so he had it just sealed off for now. Truth be told, he was more interested in knowing how they got into the base rather than why.

Arriving at the door, the guards saluted and let them in. Inside the room, pacing around and seemingly talking to himself, was a stallion who had to be The Doctor, while the mare sitting on the chair was Lyra Heartstrings. Clearing his throat, he got their attention, and The Doctor smiled quickly before walking over. "Ah, finally. Someone in charge. Been waiting for you to arrive."

"Yeah, let's just hope he's here to listen to us and not tell us the day of our trial," Lyra muttered, eyes-rolling.

"Oh, I hope not. I had to go through a trial once. Longest and most confusing moment of my sixth life. Anyway, hello, I'm The Doctor."

"Doctor Who?" Major-General Highmoor asked, eyebrow raised.

"Just The Doctor."

"Is it a code name?"

"No, just the name I go by."

"What are you a doctor of?"

"Everything and anything really," The stallion said proudly.

"Save for driving," Lyra said, rolling her eyes.

"Oi, I've gotten us to the base, haven't I? Granted, we were trying to land outside of it and speak to someone important, but this works as well," The Doctor said as he turned away from Lyra and back to the human. "So, you are?"

"I'm Major-General Marshall Highmoor of the United Nations Armed Forces, Asia Division," He answered before putting his hands behind his back and motioning to Private White Chalk. "This is Private White Chalk."

"Hello," Whitechalk replied with a nod.

"Let me guess, former school teacher?" The Doctor asked with a smirk.

"Yes, how did you know?" Private Whitechalk asked with surprise.

"Thing about pony names is that their names are usually somehow always tied to their jobs or personal talents. At least until the eleventh century when you start using more normal names. I personally like Colt Smith," The Doctor said before clapping his hooves. "Anyway, what's the situation in Osaka like so far? Any whereabouts of Fluttershy? We need to find her and Discord quickly if we're to turn things around."

"Excuse me, but you are currently under investigation for invading a restricted military base," Major-General Highmoor said with narrow eyes. "Under means, we still don't fully understand."

"Oh, that's easy. I just used my TARDIS to get here," The Doctor said dismissively. "Before you ask, it's a spaceship I use to travel between time and space. No, you can't take it apart, and no, you have no means to duplicate the technology. Also, she only answers to me. She hates it when others try to mess around with her, and she doesn't like being shared."

"...What?" Major-General Highmoor asked with utter confusion. "Time and...space? Spaceship?"

Lyra groaned and stood up. "Look, long story short, this guy?" She pointed to The Doctor, who waved. "He's a time-traveling alien from our world. Yes, he looks like a pony but trust me, he's as alien as you can get with his personality."

"Hey," The Doctor pouted.

"But he's a brilliant pony who's here to help you, and if we don't do something fast, we're going to lose Osaka. So can you please just trust us!" Lyra begged.

"You expect me to trust someone I never met before, who invades my base, claims he's some kind of alien-different from the Equestrians-with the ability to travel between time and space?" Major-General Highmoor asked in disbelief. "I don't know whether to jail you or put you in an insanity ward. Because I feel like I'm wasting my time talking to you two when I have a battle to deal with."

The Doctor rolled his eyes and leaned forward. “Listen here, Brigadier-”

"Major-General."

"Right, sorry. It's a force of habit," The Doctor apologized before suddenly looking very serious. Upon staring at his eyes, Major-General Highmoor soon paused and saw something he had seen more often than he'd like: The Stare.

The Thousand-Yard Stare that all soldiers who had fought or experienced battle beyond imagining it shocked them into a state that couldn't be described with words. Major-General Highmoor had seen such a look on his older brother when he came back from Iraq, and, despite living a good life, there was always a tiny part of him with that stare that looked like life had been sucked out of him.

This stare showed that same look but magnified a thousand times over. That was the look of someone who had fought in countless wars and seen indescribable amounts of bloodshed and death. He looked so young, but his eyes were old. Very old. Older than seemed possible. Like there was a sad and lonely person deep inside those eyes hidden behind a wall of emotions that were scrambling to protect him from being more hurt than he already was.

Most people who had such looks that couldn't pull through, in Highmoor's experience, had ended up in such depressing states they wasted away or ended themselves. The Major-General had seen many soldiers and officers, old and young, with such dark gazes but this Doctor? He held darkness in him that only a fellow warrior could see, and he nearly felt his heart collapse from it.

But as he looked deeper into those eyes, there was something more than the stare.

A fire.

An eternal fire that had no end.

A will with the power to change destiny itself.

To defy anything just to achieve victory.

Whatever darkness The Doctor had in his eyes, there was something even brighter beyond it.

For the first time, Major-General Highmoor was serious as he continued to stare at those near-immortal eyes while The Doctor spoke. "Right now, we have little time to chat or waste arguments on my sanity. Which is fine, by the way.

I'm not so old as I've gone senile. We have innocent people out there dying and suffering a fate worse than death with your soldiers, your boys and girls, doing all they can to protect them while fighting to survive for tomorrow. These people have families, loved ones, and friends waiting for them to come home so they can hug them once more.

There is a force out there, a completely misguided one, that thinks they are fighting a righteous cause when, in truth, they are being led by a madmare who is willing to burn worlds just to get her way. I've traveled all over the galaxy and time itself, fighting in situations like these because I am always determined to make sure that the people who suffer in these situations suffer no more.

I am here to save this city, and your people, so that they can have that tomorrow they wish for. Now you can help me or get out of my way because this battle will end one way or another."

"...Why should I trust you?" Major-General Highmoor asked, doing his best not to sweat as The Doctor walked over and looked him dead in the eye.

"Because I can see, through your eyes, that you are a good and honorable man, Major-General. I know your type. I know that you wish to end this battle so you can bring your troops home. So you can give care to these civilians. So you can sleep better at night knowing you did all you could to prevent further tragedy. I can help you prevent more losses, Major-General. You need a doctor to fix this mess. And me? I am The Doctor."

There was a brief silence before the Major-General sighed. "What do you need?"

"Sir?" Private White Chalk asked in surprise. "Are you sure?"

"Not entirely, but I'll take all the help I can get," Major-General Highmoor replied.

"Right now, I need to know where Discord and Fluttershy are and their situation," The Doctor asked.

"Both are in Tennōji, but we lost contact with Fluttershy. She's assisting a group of refugees with other members of the Underground Railroad, but they were being chased by a platoon of enemy soldiers last we heard," Major-General Highmoor answered. He crossed his arms and shook his head. "We have no idea where they might be going through."

"That's easy for me to figure out, thanks to this," The Doctor said as he took out a strange multi-jeweled amulet-like device. "I just needed to narrow down the area, and you just provided it. We're going on a rescue mission, Major-General. And I suggest you bring some troops with you."

"Are we expecting a fight?" Major-General Highmoor asked seriously.

"No, we're going to be setting up a trap."

+}{+

Flash Sentry had very few regrets in his life.

Leaving the Royal Guard to join the Underground Railroad was not one of them.

He had been against the entire war and the conversion potion from the start and was very vocal about it. All his life, he had dreamed of being a stallion of justice to the point that he had lived the code of the Royal Guard his entire life ever since he heard it.

Joining the elite army of honorable ponies was a dream come true, especially when he was assigned later on to be Princess Twilight's personal guard. The two of them really hit it off and fell for each other, but he had been hesitant to act on such a relationship due to their status. Fortunately, Twilight kissed him first, and he soon returned those feelings. It honestly seemed like everything would be perfect as he had his dream job, a dream girl, and a bright future.

However, their arrival on Earth had been a wake-up call. The near-zealous hatred Equestria and her leaders had for humanity had been a terrifying one to experience. Flash Sentry never saw humans as anything more than another species.

Having grown up in a multi-racial town with many immigrants from outside of Equestria, he had a more open view of the other races than most ponies did. It was sad that the average pony was slightly xenophobic, but it seemed to increase ten times when they arrived on Earth.

Even Twilight seemed to eventually believe that the humans were a lost cause thanks to her failed tour promoting Friendship with her friends. Then the situation got worse with the barrier, conversion bureaus, and now the war.

All of these actions Flash Sentry was against from the very start. He refused to believe that Equestria couldn't do something about the barrier when they had access to some of the most powerful magic users in history. The newfoals, victims of the conversion bureaus and its potions, were not normal. They were like mindless zombies with smiles and cheerful personalities that never seemed to end. They were just wrong.

And the war?

The war where Princess Celestia essentially declared a crusade against an entire race for daring to live their own lives and wanting to be who they were born as? There was no justice in this war, no righteousness in Equestria's cause, and no honor in their methods.

It was genocide. Pure and simple.

Flash argued about it with everypony. Even to his marefriend, but Twilight refused to see the truth. She, and so many others, were blinded by their love and adoration for Princess Celestia and "Harmony" that they forgot what harmony really was about. This made him lose friends quickly, with warnings from his superiors that he needed to stop the treasonous talk. But he refused. He believed in justice and was loyal to Equestria, but Equestria was no longer faithful to the ideals it once really believed in.

A crossroads came to Flash Sentry. His perfect life or his principles. He knew his choice and told Twilight he was breaking up with her and leaving the guard. That led to an argument, and...in the heat of the moment...he hit her.

That had been a regret.

He was lucky that Shining Armor and Spike didn't kill him. Perhaps they wish they did since he was now on the other side, fighting for humanity and what was right. Only now, he was possibly facing his end as he watched the ponies hunting them down, coming down the street toward the abandoned mall his group had taken to hiding under. "They're persistent. I'll give them that. How many do you count?"

"Twenty...including Big Macintosh," Dinky Hooves, a younger ex-guard, answered.

Dinky, her mother, and their friend Carrot Top had been part of the latest group of refugees seeking to leave Equestria. Osaka was supposed to be their final stop, but the battle happened. They already lost a lot of ponies, both refugee, and underground members, to the point where it was now just him, Dinky, Fluttershy, and Discord left to protect them. Discord, however, had to aid the rest of humanity's forces in the war while he and Fluttershy had guided what few refugees were left to safety. Of course, they had elderly and little ones with them, which required them to rest. This mall had been a good shelter for now, but their pursuers had come.

"Applejack's brother? I didn't know he joined the war," Flash Sentry asked in surprise.

"Many Apples joined the war recently," Dinky muttered with disappointment. "I just find it hard to believe he would even do this since he's always been a peaceful stallion."

"You don't have to help, you know," Flash Sentry warned as he turned to the young mare. "I know you were an ex-guard like me, but this is most likely not going to end well. You have a mother worried about you."

"If I don't do anything, both my mother and I will end up captured or worse at their hooves," Dinky argued with a heavy sigh. "If I'm going down. I want to go down fighting."

"Alright, then let's do this. Stick to the plan and let's hope we can take them down together," Flash Sentry said as Dinky nodded, and the two left their hiding spot to get to work.

+}{+

The small platoon of all Earth Pony soldiers smashed the near broken automatic doors of the mall and went into formation to make sure there were no threats. Among them was the oldest of the Apple Siblings in Ponyville, Big "Jay" Macintosh, who was now going through his first battle.

When he joined the army, he did it because he felt like his duty was to help defend Equestria from the humans. The news and stories he heard of their ruthlessness had nearly made him shiver with terror, and the stories his sister told of him back when she came back from that world tour with Twilight only soured his opinion more. His wife, Sugar Belle, had urged him not to join out of fear of losing him, but Big Mac had to do this as much as he loved her.

His family was out there fighting, and he wouldn't be a yellow-bellied coward for staying home. Besides, the war effort had taken a toll on the family's farm. With most of its products being used to supply the troops on the front lines, money was tight. Joining the army benefited a nice paycheck to keep his family well funded.

Still, if he was being honest, Big Macintosh didn't imagine war would be this...brutal.

The death and carnage that lay in the wake of all that had happened in his first real battle had nearly made the strong-hearted farmer throw up. He had never seen corpses before, save at funerals, and to see so many with missing limbs, eyes wide open, mouths covered with flies, and the smell of waste coming out of their bodies? It was taking all his willpower to just push those thoughts aside.

It made him even wonder if he could even kill a human if he had no choice, but all he had to do was remember the fate of his family should Equestria lose the war. Just thought of his sisters or wife being murdered, raped, or turned to glue was enough to cast aside all doubt and replace it with rage.

"Clear, sir!" One of the other soldiers reported as their Sergeant, Black Iron, walked inside. The Sergeant was a good man. About as tall as Big Macintosh due to coming from a mining family, Sergeant Black Iron was black coated with a grayish mane and tail that was short for practical purposes. His cutie mark was an iron pick over a steel ingot, and his armor was that of a shinier gold caliber with a prized blue star on his shoulder to symbolize his rank.

"We're sure the Pegasi scouts caught wind of the traitors heading here?" Sergeant Black Iron asked as one of the other soldiers nodded. "They must be hiding. Spread out. Keep your guard up."

"Sir, they're just civilians. I highly doubt that they're going to be-"

SNAP!

The sound of a broken chain forced everyone to look up and gasp as a giant display screen from above the mall's entrance started falling toward them.

"Scatter!" Sergeant Black Iron shouted as he dived to the left. Others did so, but three soldiers were unlucky as the large object smashed down upon them. Their cries of pain were short before they went silent as their comrades watched in horror as their mangled bodies, pierced by glass and metal, lay buried under the broken electronics.

Big Macintosh turned away in disgust by looking up, but he saw a figure flying above towards the east direction of the mall, where an escalator awaited them to take them to the second floor. "There! Enemy Pegasus at nine o'clock!"

"Follow him!" Sergeant Black Iron shouted as the entire patrol galloped down while the pegasus flew even faster to avoid him. "Anyone recognize him?!"

"Yeah!" Big Macintosh shouted with a growl as he recognized the cutie mark when the pegasus turned. "It's former Lieutenant Flash Sentry! He was once Princess Twilight's guard and coltfriend before he betrayed her and joined the Underground Railroad!"

"The Princess has ordered him to be captured alive! But we can still cripple the bastard's wings!" Sergeant Black Iron shouted as he continued to lead the troops. However, the sound of gunfire made him skirt to a halt just in time for a bullet to miss him and land inches from his hoof. "Shooter! Take cover!"

He was two seconds too late as more shots were fired, which resulted in two more of their soldiers getting shot. One got a bullet right in the head and went down like a lump of lard, while another screamed in agony as his bullet ripped through his two front hooves. Big Macintosh grabbed him by the neck and dragged him behind a broken electronic map helper while others took cover.

The wounded Earth Pony was sobbing as his hooves looked ready to fall off from the impact, and he soon fainted from the blood loss. Big Macintosh cursed and quickly put the wounded pony on his back before rushing back the way they came. Thankfully, the shooter wasn't firing at him, and he was able to get to their medical officer quickly to lay the wounded pony down. Nodding in thanks, the doc went to work on helping their wounded comrade.

"Horseapples! There are humans here too?!" One soldier asked as he winced from the gunfire on his protective spot behind a steel mall bench.

"I'm seeing a horn glowing. Must be a unicorn!" Another soldier shouted. "Second level! By the escalator!"

A clank was heard, and a pop of smoke went off that covered their vision. "Damnit! Smoke grenade!" Sergeant Black Iron shouted as he turned around and looked at his unit. "Jade, Sunrise, Macintosh, Chaser, and Bouncer! You five go back the way we came and see if you can get around this shooter! Keep your flanks low!"

"Yes, sir!" Big Macintosh shouted as he and the four others who were called rushed down the way they came.

+}{+

Dinky sighed as she rearmed herself with another clip for her M16A2 with iron sights. The one great thing about being a unicorn was that you could use firearms thanks to magic. Of course, you still had to learn how to properly use them and not shoot yourself or anyone else like a dumbflank.

When she went to the human world for the exchange that one year, she learned gun lessons from an NRA club that Tom took her to once. There was something extraordinary and awe-fearing when you used a powerful weapon such as a gun, but it was not a toy. It was meant to be used to protect and kill if necessary. Something Dinky had no problem doing as she was trying to protect her mother and all those fleeing from the nightmare that had become their home.

And she was willing to kill anyone who threatened them.

Flash and Dinky knew that this wouldn't hold them off for long. They could find another way to try and flank them, but she trusted Flash to deal with them. Snapping her clip in, Dinky waited for the smoke to clear and started firing again. This time, she hit a few more of her targets, but this did little to prevent the others from fleeing. They were determined to get to her and avenge their comrades.

What's worse was she didn't have a lot of ammo left. The fights for survival earlier had drained her of most of her clips, so she had to make every shot count. However, one of the guards got smart and used their great Earth Pony strength to pull out one of the mall's electronic advertising boards and hold it up for a shield. Cursing, Dinky fired shot after shot at the stallion, who continued to hold his makeshift shield as others formed a line behind him. Even after a few of her shots punctured through and hit him, he gritted his teeth and continued until he was close enough to the escalator and collapsed with a final grunt.

Cursing, Dinky knew she had to fall back. However, she knew that the Earth Ponies would outrun her due to their incredible stamina and prepared herself for CQC. Just as the soldiers began to climb up the escalator, a whirring sound caught Dinky's attention. That was soon followed by gears moving and ponies yelping in surprise.

A stunned Dinky looked down in confusion as the escalators soon activated and, at rapid speeds, sent the soldiers straight downward in a heaping pile as their armor clashed against one another, and they fell into a pile. A few tried to get back up the escalators and outrun them, but they weren't fast enough (not to mention it was more complicated with hooves instead of feet), and they fell on their faces and bottoms.

"W-What?" Dinky asked, blinking in surprise.

"You know, I believe the sign says that running up the escalators is a safety hazard. Maybe because it's in Japanese, they couldn't read it." Dinky turned around with a yelp to see a smiling pony with a glowing metal stick in his hoof nodding to her. "Hello. I'm The Doctor."

"Who?"

"Me," The Doctor said as he looked down at his work. "And they will be preoccupied for a while, so let's go check on your friend and make sure he doesn't get into any trouble, shall we?"

Dinky blinked and shook her head while holding her hoof up. "Wait a minute! You're The Doctor? The one that Princess Celestia put an Automatic Kill Status on for unknown reasons? The Number One Enemy of Equestria even over Fluttershy and Discord?"

"And that's another on the list of races with me as their number one enemy," The Doctor chuckled. "But yes, I am The Doctor. I didn't know I was famous already. Anyway, we should go. I know you don't trust me but-"

"Okay, let's do it," Dinky said with a nod.

"...well that was fast," The Doctor said with a blink. "Just like that? I don't have to give a speech or something about me being trustworthy, wanting to help humanity, end the war, blah blah blah?"

"Both of us are Sunbutt's enemies. That alone makes you trustworthy," Dinky said with a grin as she turned around and aimed her gun at the soldiers who were still trying, and failing, to get up the escalator. "Let me just take care of a few more of-"

"Nope!" The Doctor said, taking the gun and tossing it away. "No need for that. Trust me. We can defeat these soldiers without losing more lives."

"But-"

"Tally ho!" The Doctor said, taking Dinky by the hoof and dragging her away.

+}{+

"They're getting away, sir!"

"I know that, you idiot!" Sergeant Black Iron shouted as he stared at where the unicorn and the strange Earth Pony were before they fled. "Forget the escalators! We'll find another way up to the second floor!"

"Sir! I think this elevator is still working!" Another soldier shouted, pointing down the corridor where a lit-up elevator was waiting for them, open and everything. "Looks like we can all fit in here!"

"Great! Let's go! Doc? Stay here with the wounded until we return!" Sergeant Black Iron shouted as all of what remained of their group went inside. The last pony in pressed the up button, and they waited for the doors to close before the machine started slowly moving. Suddenly, halfway up to the next floor, it jerked and halted.

"What the?" Sergeant Black Iron asked in surprise before the speaker suddenly turned on.

"Hello! This is a recording from The Doctor. If you soldiers of Equestria used this elevator, or any elevator in the mall for that matter, please rest assured that no harm will come to you. You are merely just trapped, thanks to some hacking, for the duration of whenever I choose to release you. By then, U.N. soldiers will be ready to properly take you into custody, where you will be treated fairly as POW's. Please do not resist, as I hate to see more wasted lives, and I doubt your families want you to die. So sit tight and relax to some soothing elevator music."

A calming tune began to play over the speakers as the stunned Earth Ponies just stood there in silence upon realizing they had been trapped. Sergeant Black Iron facehoof and knew his career in the army was over.

Can this be any worse?

"...I have to go to the bathroom."

Ughhh......

+}{+

The sound of gunfire made a few of the refugees jump, but nopony spoke a word out of fear of being found. A few of the foals let out whimpers as their parents tried to comfort them, while others silently sobbed.

They had decided to hide in the back of a yakiniku restaurant's kitchen in the hopes they could hide well enough from the troops chasing after them while Dinky Doo and Flash Sentry personally went out to deal with them. Fluttershy sighed in despair as she looked at the ponies she had been charged with protecting and felt like she had failed them.

This was supposed to be a peaceful stop before arriving safely in a place where Equestria wouldn't find them. She underestimated just how far Twilight was willing to go to capture her. They had already lost so much from the violence. Some even just gave up and could go no further, and the shy pegasus could only pray that they were being treated right.

And Discord?

He was fighting with all he had out there.

"I can't help but feel this is all my fault," Fluttershy whispered to herself but quickly felt a hoof on her shoulder. Turning around, she saw a smiling Derpy Hooves and Carrot Top looking at her.

"It's not your fault, Fluttershy," Derpy replied as she hugged the sniffing pegasus. "We all knew the risks when we asked to leave Equestria. We made this choice. You're doing the right thing."

"But still..." Fluttershy shook her head. "Your daughter is fighting out there and could die....maybe if I give myself up-"

"No," Derpy said, putting a hoof on her lip and shaking her head firmly. "My daughter is like her father. She believes in justice. What she's doing right now is no different than what she was doing when she was back on the guard. I know there is a risk I can lose my daughter, but I know that everything is going to be okay." She smiled at her warmly and winked. "We'll be fine. Trust me."

"Yeah, and besides," Carrot Top put up her hooves and punched them in the air, "I'm not a slouch of a fighter myself. I won the Golden Hooves Amature Boxing Tournament in Ponyville three times running, you know?"

"Weren't you disqualified the third time because you got drunk before entering the ring?" Derpy asked, tilting her head as her eyes went in different directions.

"Hey, I still won."

Fluttershy giggled as she felt a part of her despair fading until she heard hoofsteps entering the establishment, and it made everypony go silent. She held her breath and gulped before stepping forward towards the kitchen's opening doors, hoping to get a peek at whoever was there.

"Hello? Fluttershy?"

Wait a minute...that voice! Fluttershy gasped as she nearly smashed the doors open and gasped in surprise upon seeing an equally surprised mare that Fluttershy hadn't seen in a long time save for wanted posters. "Lyra!"

"Wait, Lyra?!" Derpy and Carrot Top rushed out and were in awe as the infamous unicorn walked over and hugged the three.

"Thank goodness we've come just in time!" Lyra said as she ended her hug and smiled at the three. "Are the others with you?"

"Almost everyone but Derpy's daughter and Flash Sentry," Fluttershy replied as she looked around. "Is it just you? Wait, how did you get here in the first place?"

"I hitched a ride with a crazy stallion in a box," Lyra said with a smirk. "But yeah, I brought help. Don't worry, everything's going to be okay."

+}{+

Big Macintosh and his troops were almost to his location. Flash Sentry sighed as he realized that this would be a tough fight. He might have been outnumbered, but he had experience and skill while most of these guards were rookies. He personally had been trained, and became friends with, Prince-Consort Shining Armor back in the days when he was welcomed by the Sparkle Family as a member of their clan when it looked like things were getting serious between Flash and Twilight. Despite having no regret in his choice, Flash wishes things hadn't become so bitter between him and his former special somepony.

He was waiting for them in the middle of the food court, and it didn't take long for them to come up the escalators to find him waiting for them. Big Macintosh was leading them, and he narrowed his eyes at Flash Sentry, who calmly looked at him. "Flash."

"Big Mac," Flash Sentry asked before sighing. "How's your family?"

"Fine, but Ah can't say the same for yers, traitor," Big Macintosh growled as he pointed at them. "After ya turned tail on your home, yer family was so ashamed they pretty much disappeared from the face of Equestria."

More like the ESS had their way with them, Flash bitterly thought.

"Ah thought yer were a good pony when Twilight introduced ya to all of us," Big Macintosh sighed. "Guess Ah was wrong. Ya really hurt her, Flash. Ya hurt us all. You betrayed Equestria."

"No, I didn't betray Equestria," Flash Sentry started with a firm tone. "Equestria betrayed itself."

"What are you talking about?!" Another one of the soldiers asked in disgust.

"Equestria used to be the nation that promoted peace, harmony, friendship, and justice. I was raised to believe in these things and lived them as best as I could.

But what happened when we came here? I saw hatred, fear, paranoia, injustice, and war. I saw a society condemn an entire race just for the crime of living their lives differently while challenging thoughts we never once questioned our entire existence, which opened us up to new concepts our Princesses feared.

I watched the home I love, with ponies I knew my entire life, outright boast how superior they were with such pig-headedness I'm surprised our heads didn't explode. I watched as the love of my life, the stallion I respected, and the princesses I worshiped fall from grace and turned into the shadows of the great ponies they once were." Flash closed his eyes and took a heavy sigh.

"I could have just obeyed orders. Been a good little soldier and just follow along. But that's not me. It's not me being loyal to the ideals I've come to follow. It's not being loyal to who I am deep inside. And it's not being loyal to the real Equestria that's been replaced with this disgusting shell of its former self."

Clanking his armored hooves together, Flash Sentry flares his nostrils and spreads his wings. "I'm not a traitor, Big Mac. I am a loyal son of Equestria. And if that means fighting her to save her? So be it!"

Suddenly, there was clapping.

"Bravo! Excellent! Well said, Sir Sentry!"

Everypony turned to the right to see Dinky and a strange earth pony in a blue coat smiling as he clapped his hooves. He pulled out a peculiar amulet with multiple gems on it, with the red one glowing while he pointed it at him. "I dare say, I was expecting to find one of them here but never imagined I would find two. Seems luck is on our side today."

"Who are ya!" Big Macintosh demanded while stomping his hoof.

"I'm The Doctor, and I'm here to request your surrender," The Doctor said as he nodded in greeting. "The rest of your comrades are either dead, too wounded to fight, or currently trapped in an elevator if my Sonic Screwdriver's readings are right, but they have enough oxygen to last for a few hours, so they should be fine."

"And you expect us to surrender just like that? We outnumber you, and you have no weapons," One of the soldiers stated.

"Well, technically yes on those two points," The Doctor said with a shrug. "You outnumber us, and we have no weapons...but those points don't necessarily apply to these folks."

Without warning, dozens and dozens of armed U.N. troops burst out of hiding from around the food court's multiple food stands. From McDonald's to Matsyua, heavily armored and equipped humans stood in position and aimed their guns at the shocked Earth Ponies. Even Flash Sentry and Dinky were surprised by the arrival of all these humans.

"H-How?! How did you get here so fast?!" One Equestrian soldier asked in disbelief.

"You wouldn't believe me even if I told you," Major-General Highmoor stated as he walked out beside his men, arms behind his back, and shook his head in amazement. "I thought I'd seen it all before when your kind arrived...but that box? Something amazing."

"Yes, she's never had that many people inside her before," The Doctor said with a nervous chuckle. "Hope she's not too mad at me when I go back inside."

"Anyway, I suggest you surrender, Equestrians," The Major-General said firmly. "You are currently outgunned, surrounded by all sides, and you have no reinforcements with your other comrades currently detained until we can properly take them in. I promise that you will be treated fairly under the Geneva Conventions rules."

"Why should we bother taking these ponies alive?!" One human soldier growled as he aimed his gun a little higher. This made others snap their heads to him. "All those innocent people...civilians...children...all of them are dying or worse because of them! Why should we show them mercy when they've been nothing but monsters?!"

Before The Major-General could tell his man to stand down, The Doctor coldly interrupted, "Because then you become what they see you as."

Everyone turned to him as The Doctor glared with such a stern look the soldier nearly dropped his gun. "Right now, the Equestrian Government has been filling these ponies with lies stating that you are all demons who wish to destroy everything and anything around them. You are evil incarnate and have no concept of mercy, love, or kindness is something everypony from the youngest foal to the oldest senior citizen is being told repeatedly without stopping.

And this is not true.

I've only been on this planet for a short while, but I've seen the goodness in your race. A race with great potential." He glared at the Earth Pony soldiers, who gulped upon seeing his cold and icy stare. "In many ways, they are victims too. Filled with lies and paranoia, they cannot see the truth that has been blinded to them like a curtain on a window. They think the worst of you and, naturally, you think the worst of them. But that's always how the cycle of violence continues.

Hated met with hatred.

Fear met with fear.

It keeps the wars, battles, and purges going on endlessly, no matter how many lives it ruins. I've traveled throughout time and space, and I've seen these situations more times than I ever wished to count."

He walked forward until he was in the center of the entire room, looking at everyone who had stopped thinking just to hear his voice. "I understand that one must be ruthless with war. And evil must be stopped. But there comes a time for mercy. A time for kindness. Because that's what ends the wars.

That's what ends the hate.

One single act of genuine kindness and trust can shatter the will of a million soldiers if they are proven what they were fighting for was all a lie. You can kill them, sure, but will that solve anything? You would be killing defenseless and defeated soldiers in the name of revenge, but then you prove to Princess Celestia that she was right about you.

Because while you may be thinking about your friends, family, and loved ones, they are also thinking the same. Ponies they care about who are praying they come back alive. I know you are scared. Just as they are scared. But the only way this fear and hatred ends is if we stop to open that curtain just for a single moment.

We expose them to the sunlight.

Maybe then this war can end faster. I am here to stop Equestria from destroying this world, and I will be ruthless and violent when I must when the situation calls for it. But this is not that time. This is a time for mercy. So don't be what they think you are. Show them what you really are."

There was a long silence as everyone, pony and human, stared at The Doctor, who stood there with unflinching determination. Finally, Big Macintosh sighed and slowly took off his helmet. "If...if ya really are gonna show us mercy...then we surrender."

"...Captain?" Major-General Marshall Highmoor ordered as he summoned a soldier to his side. "Take your men and secure the prisoners. I want them unharmed and treated well. Give them water too. Also, send a detachment to pick up the other enemy soldiers."

"Ah'll go with ya," Big Macintosh said, getting a raised eyebrow. "It might calm them down more if somepony from the unit was there to convince them."

The Major-General nodded as he soon gave out more orders to secure the mall and sent up sentry points while requesting an evacuation. He walked over to The Doctor, stared at him, and saluted. "Well, Doctor. If I had any doubts, they were gone now. Know that you have a friend in the U.N should you need me."

"Thank you, Major-General, but the battle is far from over," The Doctor said as he turned to Flash and Dinky. "Take me to see Fluttershy really quick."

"Why?" Flash Sentry asked.

"Because we're going to save Discord."

Author's Note

And here we go with part 4. Be sure to help out at the TV Tropes Pages for the Negotations_verse series: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 5

“There is good and there is evil. I left Gallifrey to answer a question of my own. By any analysis, evil should always win. Good is not a practical survival strategy - it requires loyalty, self-sacrifice and love. And so, why does good prevail? What keeps the balance between good and evil in this appalling universe? Is there some kind of logic? Some mysterious force?”

The 1st Doctor

+}{+

Fluttershy had been surprised but grateful to see the U.N. soldiers arriving to help them. She learned that Big Macintosh and the rest of their unit had surrendered peacefully without any more loss of life. Although Fluttershy knew she was now part of a war, that didn't mean she enjoyed seeing death befall anyone, regardless of the side it fell under. Especially from those she once called friends.

The Element of Kindness watched as the various Earth Pony soldiers, stripped of their armor, were being held in a line in cuffs thick enough to keep them from doing anything rash just in case. Numerous Osprey had arrived to start escorting the prisoners and the refugees from Equestria to safety. The former calmly did so though they weren't happy about being captured based on their expressions. She even saw Big Mac glance at her, but he only sighed and turned away before being led by his fellow soldiers. Perhaps when this was all over, she could talk to him?

Meanwhile, the ponies that had been her charge from Van Hoofer to here in Osaka all looked at Fluttershy with grateful eyes and thankful expressions before they were sent off into safety. The only ones who refused to go were Derpy, Dinky, Flash Sentry, and Carrot Top, all because they wanted answers regarding their saviors.

Seeing Lyra again, alive and well, was a relief for Fluttershy. She had always felt that, deep down, Lyra was right about humanity but Fluttershy had been too afraid at first to say anything since she was scared of alienating her friends. The war, however, made that fear slowly fade away and replaced it with a resolve to do what was right instead of doing what was expected. When Discord begged her to leave Equestria, and she saw the seriousness in his eyes, the Element of Kindness knew it was finally time to go. Learning what happened to their old-world only solidified her determination to end this war and stop Celestia.

Fluttershy still couldn't believe that the princess she had admired, respected, and loved for most of her life was such a monster. This was the princess who had playfully let her hang out with Philomena. The same one who held faith in her redeeming Discord. And the one who treated her as part of the family during celebrations and events. It just made no sense to Fluttershy why Princess Celestia would be so...heartless and cruel, but sometimes the truth was too hidden to see.

Pushing aside her thoughts, Fluttershy and her companions soon found themselves meeting the strange stallion who had been the one that had changed so much in such a short time: The Doctor.

The one who Discord was most afraid of and told Fluttershy that he was beyond understanding. Yet this one being, who made her best friend weak in the knees, looked like any other stallion she had ever met. He talked to the Major-General for a bit before Lyra finally got his attention, and he eventually turned around and saw them. That's when Fluttershy looked into his eyes...

"Fluttershy? Are you...crying?" Flash Sentry asked, getting everypony's attention as she just stood there, sobbing silently as she stared into the confused Doctor's eyes.

Fluttershy had always known she had a unique talent for seeing aspects of all sorts of creatures through their eyes. It worked on ponies as well, which is why she could always tell a stranger's best and worst characteristics by looking directly at them.

When she looked at Twilight, she saw wisdom, excitement, passion, and a gentle soul who was lonely at times because she felt so different from others.

Rainbow Dash? Determination, bravery, a fear of failure, and a need to stand out to prove she was somepony and not a nopony.

Applejack was similar to Rainbow Dash but had more confidence, and heartache from the losses she had suffered at a young age that drove her to work hard.

Rarity was beautiful on the inside as she was on the outside. She was a charitable and loving soul that wanted to unleash the true potential of not just those around her but also in herself. Yet, there was a particular obsession with this mindset that was somewhat scary.

Pinkie Pie was harder to look into as you could see the joy, happiness, and fun in her eyes, but there was also a hint of madness, sorrow, and something darker hidden behind it.

Others she couldn't really read, like Princess Celestia, Luna, or even Discord at times, but she could get glimpses of how lonely they were deep down inside

And when she looked into The Doctor? All she could do was ask one question.

How?

How could somepony like this live with what was inside them?

There was so much pain.

So much sorrow.

So much fear.

It was like looking into a black hole that swallowed everything. Fluttershy wanted to run. Run away and never look at anything again, but she couldn't. The amount of darkness this pony had seen was enough to make her heartache.

And yet...there was something else.

There was kindness.

There was courage.

There was determination.

Most importantly, there was hope. Like a supernova bursting inside that swirling cyclone of darkness. A light that refused to go out no matter how dim things were. A force of will that continued on despite having lived for so long. Because it was searching for something. It was trying to prove something. It was like looking into the heart of meaning itself.

He held so much struggle in his soul, yet you couldn't tell by just looking at his confused face. One that had a smile that spoke both a lie and a truth. So Fluttershy did the only thing she could do. She ran up and hugged him.

The Doctor was shocked, but she whispered only two words when she looked at him with her crying eyes. "I'm sorry."

At that moment, he went silent and realized she knew.

She may not have known how, why, or what was behind his eyes, but she didn't care. She felt it. And this creature was perhaps the most amazing and tragic figure in the universe for having that burden. Pressing her head against his chest, she whispered again, "I'm so sorry."

"... It's alright," The Doctor whispered as he stroked her hair and slowly looked at his amulet, which showed the green jewel glowing. "I'm used to it."

That only made her cry harder.

+}{+

"Holy manure!" Carrot Top cried out as they all entered the TARDIS together. "It's bigger on the inside than it is on the outside!"

The Doctor smiled as his newest companions all stared in awe at the TARDIS while Lyra just smirked and asked, "Is everypony always like that when they come in here the first time?"

"Pretty much," The Doctor said as he chuckled and pressed a few buttons. "And they always say that same line. Well, sometimes they say it differently like Clara did."

"Another of your past companions?" Lyra asked curiously.

"Yes, but..." The Doctor paused and took a deep breath. "Not one I want to think about at the moment."

Lyra blinked and then looked around the TARDIS as the others continued to look around in awe. Flash Sentry and Dinky were checking out the tactical map of the current war around Earth while pointing at various locations.

Carrot Top was gazing into the glowing white circle lights and probably wondering what they were used for (Lyra sometimes wondered the same thing). Fluttershy looked into the other corridors with wide eyes, no doubt wondering how far the TARDIS really went. Derpy was over at the tea set happily eating a pair of muffins that had just appeared out of nowhere, so Lyra chalked it up to something the TARDIS did.

"Have you ever had this many ponies in your TARDIS before?" Lyra asked as The Doctor continued to work.

"Not often," He admitted with a shrug. "There was that time in my tenth life when I had to stop Davros and the Daleks from stealing Equus and using it to destroy the universe. That was a hairy situation."

"...And they didn't stay with you?" Lyra asked, which made The Doctor pause. As Lyra sighed and asked, he stood there, frozen, "Doctor? What happens to your companions? You said it yourself. You're very old, but you talk about all your past companions like a grandfather talks about his children. Yet, you always seem to be so alone. What happened to them?"

Lyra worried she said something wrong for a moment, but she was too curious. The Doctor had spent two thousand or more years wandering the galaxy of their old dimension, fighting evil and saving lives.

"But never alone! Always with someone! Others who I am proud to call my friends, comrades, family, and more! The Doctor and his Companions! Legends throughout time itself!"

That was what he said to her.

Sighing, The Doctor gave a sad smile as he looked at Lyra and shook his head. "They never stay forever. I'm a Time Pony, Lyra. I don't age. I regenerate. Even more so now that I'm pretty much unable to stop regenerating. Don't ask. It's a long story. At some point, the adventures I have with those I travel with come to an end."

He closed his eyes. "Some...had to be left behind so they could grow up..."

***

“During all the years I've been taking care of you, you in return have been taking care of me.”

“Oh, Grandfather, I belong with you!”

“Not any longer, Susan. You are still my grandchild and always will be. But now, you're a mare too. I want you to belong somewhere, to have roots of your own. With David, you will be able to find those roots and live normally like any mare should do. Believe me, my dear, your future lies with David and not with a silly old buffer like me. One day, I shall come back. Yes, I shall come back. Until then, there must be no regrets, no tears, no anxieties. Just go forward in all your beliefs and prove to me that I am not mistaken in mine. Goodbye, Susan. Goodbye, my dear.”

***

“Others were taken away against their will...”

***

“Goodbye, Jamie.”

“But Doctor, surely we can't just-”

“Goodbye, Jamie.”

“I'll never forget you, you know.”

“I won't forget you! Goodbye, Zoe.”

“Will we ever meet again?”

“Again? Now, Zoe, you know that time is relative.”

***

“Others realized they couldn’t stay forever, especially when they wanted something more...”

***

“Because the thing is, it's like my friend Vicky. She lived with this bloke, student housing, there were five of them all packed in, and this bloke was called Sean. And she loved him. She did. She completely adored him. Spent all day long talking about him.”

“Is this going anywhere?”

“Yes. Because he never looked at her twice. I mean, he liked her, but that was it. And she wasted years pining after him. Years of her life. Because while he was around, she never looked at anyone else. And I told her, I always said to her, time and time again, I said, get out. So this is me, getting out.”

***

“A few couldn’t stay anymore because it all became too much...”

***

“My Aunt Vanessa said, when I became an airline stewardess, "If you stop enjoying it, give it up."

“Tegan...”

“It's stopped being fun, Doctor! Goodbye.”

***

“Some died...”

***

“…Adric…

***

“Some were lost...”

***

“You look after him, and you be a good girl, and you look after him.”

“You are creating a fixed time. I will never be able to see you again!”

“I'll be fine. I'll be with him.”

“Amy, please, just come back into the TARDIS. Come along, Pond, please.”

“Raggedy man...goodbye!”

“NOOO!”

***

“And others... well...”

“Dear Doctor. It’s been such a long journey for both of us. I never, ever wanted it to end, but end it has. We both know that. A long time ago now, I said you were the oddest man I’d ever met. You’re that still. You’re the best stallion I’ve ever met too. But we’ve chanced our luck once too often, I think, so I’m bailing out. Escape strategy number five. I’m going to disappear. There’s no freedom like being dead. I can go anywhere, be anyone I want. Just like a Time Pony really. Don’t look for me, please. But remember me. I’ll remember you, always.

With love, The Filly Who Never Was.”

***

“But some...went on to find happiness...”

***

“Don't go too far away, will you? And if you do, come back and see us sometime.

“Yes.”

“Thank you. Lovely.”

“Save me a piece of wedding cake. Oh, I nearly forgot. Your wedding present.”

“It's beautiful. Thank you, Doctor.”

“Hey, Jo, come and drink a toast to the happy couple.”

“But that's us!”

“Aye, so it is. Don't worry, Doctor. I'll look after her.”

***

“Others needed to leave to continue their lives...”

***

“You’ll come to our graduation, won’t you, Doctor?!”

“Of course, Silvy. Wouldn’t miss it for the world.”

“So long as the world isn’t at risk of being blown up, right Doc?”

“Yes, Gallus. We’ll try to avoid that next time.”

***

“Some are waiting for me to come back...”

***

“Do you really have to go, Doctor?”

“Sorry, Izzy, but I have to check up on something. But don’t worry. I’ll be back soon. Be in a minute, day, week, month or year? I will return. And the six of us will have more adventures awaiting us when I do!”

“Woohoo!”

***

“And there are plenty who will always be there willing to go with me for another adventure...”

***

“Wicked...”

***

The Doctor then smiled at Lyra and chuckled. “Yet, for all the pain it sometimes brings I never regret taking any of them aboard. Because they are what makes my life feel like it means something. To think it all started with keeping two school teachers in my TARDIS out of fear of being exposed and it’s become this now. Every one of them I remember and treasure because they changed me and, in turn, I changed them. It’s not all easy and certainly I have regrets...but as one of my closest friends once said...”

***

“You know, you act like such a lonely pony. But look at you. You've got the biggest family on Equus.”

***

“...But because of what happened... on Equus,” The Doctor whispered as he closed his eyes and lowered his face. Lyra couldn’t tell, but she was sure he was about to cry or scream from the way his body shook. Maybe both. “With Equestria here...and the world gone in your timeline...most of them are lost...not all...but...too many...far too many...I want to bring them back...I need to bring them back and even if I don’t know how I’m still going to try.”

“And if you cannot?” Lyra asked.

Then he stood still, slowly raised his head, and upon seeing the look in his eyes and the anger despite his calm and stoic expression, Lyra felt nothing but utter fear and terror for a terrible split second when he heard him whisper:

“Then I will avenge them all.”

"Uh, Doctor?" Their conversation was interrupted by Flash Sentry, who was looking at one of the screens on display in the "War Computer." Everypony soon crowded it and looked in horror as it showed a drone's camera of Discord being thrown against the pavement by a combined blast from Twilight, Cadence, and Shining Armor.

"Discord..." Fluttershy whispered in horror.

"Right! No time to waste!" The Doctor shouted as he went back to the TARDIS controls and went to work before the TARDIS started to move again. "No more delays! The time to end this battle is starting now!"

+}{+

Discord always wondered when he would meet his end, and he never thought it would be outside a ramen noodle shop. The battered, bruised, and bleeding draconequus lay in a crater, breathing heavily as he looked above at the sky covered in the ashes of war. Earth had such a pretty sky when you really stopped to look at it. Sure, it didn't seem any different from the sky of any other world, and yet...

Raising his head and sitting up as best as he could, Discord glared at the three ponies who stood nearby, ready to strike. It showed how strong they had become over time and how weak he had gotten. Although he had done his best and gained a few good blows on the three, they could still go on while the rest of their squad was unconscious. Discord didn't even have the strength to summon one last glass of chocolate milk.

"For the last time, Discord. Where is Fluttershy?" Shining Armor stated as he raised his sword. "If you tell me, I'll make your end a quick one."

Discord shook his head. "I'm never going to tell you. Ever. Everything I've done has been for her. I'm not going to betray her again. Never again."

"Tell me, Discord," Princess Cadence asked as she stepped forward. "Are you doing all this just for Fluttershy? If you just care about her, then help us find her, and we can help her. She's not in the right mind if she thinks that what we're doing is wrong."

"Cadence is right, Discord," Twilight said as she pointed to the entire city. "Look, I don't like this war as much as the next pony. I can understand being afraid of what we're doing. But this is for the best. Humanity has proven they cannot continue like they are, or they will destroy themselves. We're offering them a chance to survive and live something better. We're not trying to hurt them. We're trying to save them."

"Save them from what? From having the freedom to choose who they want to be?" Discord grumbled as he slowly sat up and shook his head. "You ponies really don't get it, do you? Do you really think that your way is the best because you happen to be number one in your world? Newsflash, Twilight, you were just the top dog at the moment in history. Before you were the griffins, the dragons, the alicorns, the wolves, and the silurians. History is always about some nation losing power and a new nation regaining it. Your so-called perfect utopia would have fallen eventually, and another nation would take over. I always thought it would be the diamond dogs, but we'll never know since our world is gone."

"That's just a lie, Discord!" Twilight shouted with fury. "Princess Celestia-"

"Can go fuck herself," Discord said, which only made the three angrier, but he didn't care and smirked. "And so can the rest of you. Because you clearly are a bunch of idiots who cannot think for themselves. You're slaves to a madmare, and I hope you regret it forever when your world comes crashing down. As for me? Sure, I'm gonna die. But I'll die as myself and do the right thing."

He chuckled and shook his head. "You want to know something? I did agree to do this all for Fluttershy's sake, but knowing what I know now? I think deep down, I would help humanity even without her blessing. Because I've seen these humans in the best and worst, and I know why I like them. Why is their chaoticness so familiar to me?" He closed his eyes and smiled. "They remind me of my true home. My true people. When I see them, I see the faces of my mother, my father, my childhood friends, and more. I see their potential, even without the means to reshape reality. I saw one world burn from those who sought to destroy them because of who they were. I'm not going to let that happen again."

Pointing at the three, Discord shouted, "Because so long as I breathe, I will sacrifice everything to defend this world from you ponies! Even my life!"

The three were silent as Twilight sighed and stepped forward. With a sympathetic look, she whispered, "Goodbye, Discord."

Twilight began to shine her horn as Discord slowly closed his eyes and prepared for his end. But then...

"Excuse me!" Everypony stopped as a figure walked out of a nearby alley. At first, the ponies feared it was a human but then were confused when they saw a pony walk out with a smile on his face. "Sorry to interrupt this fight. Wow, that's a lot of cotton candy on that sidewalk. And has that shield been turned into a pear? Ugh, I hate pears. Honestly, all this violence really has ruined this nice street." He frowns as he shakes his head in disappointment. "War is just terrible all around, isn't it? You come to a new planet, a new dimension, with so much to learn, and the first thing you discover is death, destruction, and chaos. Millions of worlds are out there, and yet so many of them are always filled with bloodshed. It is a sad thing, really."

"Who are you? Are you from the Guard or the ESS?" Shining Armor asked, looking at him with confusion.

"Sorry, but no."

"This isn't a place for Equestrian citizens to stay!" Princess Cadence warned with concern.

"Sorry, but I am not from Equestria."

"Are you a newfoal?! It's not safe here! You need to get to the containment camps to be properly sent to Equestria!" Twilight warned.

"Wrong answer," the strange pony replied. "I'm not a newfoal. Not even a pony. Not really."

"Then… who are you?" Twilight asked.

The pony chuckled. "Ah yes. Who am I? The one question in the universe that I've heard repeatedly. I even had a cult try to kill me because of it. I... wasn't very nice to them in the end. Kinda deserved it. Did get married for a time thanks to them, so there is that. I wonder if River ever put this in her diary..."

"Um, are you okay?" Shining Armor asked, eyebrow raised. Shaking his head, he said, "Look, it doesn't matter. You shouldn't be here."

"Neither should you," The pony said sternly as he glared at them. Despite just meeting him, the three couldn't help but flinch at how cold the stare he gave them was. "I'm so disappointed in you three. I'm glad Sunny isn't here because if she saw you, as you are now? The poor filly's tears would never end. Especially for you, Twilight Sparkle. You know, even hundreds of years after your death, you would be remembered. All of you. All your friends, adventures, lessons, and deeds. Even after a thousand years, you would be remembered, but all of that wisdom? All those adventures you had? The teaching you discovered and, in turn, gave to the world? Wasted. All wasted. And I really can't help but feel utter pity for how far you have fallen."

There was a long silence as the strange pony continued to look at them before he took something out, some kind of amulet with multiple gems on it. He stared at Discord, looking at him with wide eyes and an open mouth while pointing the amulet at him. The light blue one was shining, making the strange pony smile brightly. "But you, Discord? They say that hard times create strong creatures. Look at you, from villain to anti-hero to hero. But this? I think this is your fondest moment. Proving that, deep down, you're a better creature than you think."

"... It's you," Discord whispered in awe.

"Yes," He replied.

"...Why weren't you there? On that day? That day I lost everything?" Discord asked as he slowly lowered his head and sobbed. "My father. My mother. All of my people..."

The pony sighed in such a way that it reminded the other ponies of how Princess Celestia sighed only because he sounded much older for some reason. The mysterious pony knelt before him and lifted his head up. "Much as the legends like to make me seem like I am a god, the truth is I am not. I am just one old stallion in a box that can only do so much. But when I am there...I always do my best to make others smile. I couldn't save your people, and I am so sorry that I can't bring them back. But I can give you something else. I can give you a future."

"But we changed the future..." Discord whispered in confusion. "The timeline it's...gone..."

"So let's rebuild it or make a new one," The stallion replied with a nod. "It will take time. Maybe it won't ever be like it once was. But if there is one thing I have learned in all my travels, it is that when the dust settles and the nightmare is over? You can rebuild and start again. But only if you let go of the past." He held out his hoof. "There is a mare out there waiting for you and others. And...there was also a stallion... you'd like him...brave and strong...a truly loyal and kind friend...stubborn at times, so narrowly focused on what he thinks he ignores what's around him, and sometimes kind of an idiot, but when you get down to it? You couldn't ask for a better sheriff."

"Who is he?"

"Somepony that doesn't exist now, sadly. But there is a chance for him to come back so long as two certain individuals are alive and well. Because that pony? Far off into the future? His favorite drink is chocolate milk, and animals love him," He answered with a smirk. "So much so that he can understand what they are saying."

Discord slowly looked up and stared at the pony before laughing. He laughed and shook his head before tears began to fall down, yet he still laughed. Discord then took a deep breath. "What's his name?"

"Hitch Trailblazer. Well, Sheriff Hitch Trailblazer if you want to be technical," The stallion said as he helped the chaos spirit up. "And I don't know if I can bring him or those wonderful mares he called friends back or anyone else lost in our old dimension. But I won't stop trying. I never will. And if I cannot? Well, then I'll just try again."

"...So there is a chance?" Discord asked with hope in his heart.

"Always a chance," The stallion said with a wink. "Always time for one."

"...Could somepony explain to me who the buck you are?!" Shining Armor asked, which made the stallion moan.

"Seriously?! We're having a moment here! But if you want to know who I am?" The stallion then marched towards them with a severe glare as his coat raised from the windy breeze. "I happen to be a citizen of the universe that goes wherever I want.

I've traveled through every corner of the galaxy, both past, present, and future.

I've destroyed monsters, brought justice to evil, and stopped the ends of thousands of planets, including yours.

I've been to the darkest places where unimaginable horrors await, and I've seen the birth of new life from its origins.

I've been a warrior, a poet, a healer, a savior, a traveler, a teacher, a husband, father, grandfather, companion, friend, and more words beyond counting.

I'm very old, but I always look younger than I'm supposed to.

I've changed shape, gender, size, race, attitude, likes, dislikes, habits, and more, but my morals and principles have been as unyielding as the universe's expansion.

I keep moving and never look back because I can't.

I do the things needed in our universe, this universe, or any universe because someone has to. And right now, the people of this planet need me.

Who am I?

I'm The Doctor.

And I'm here to stop you."

The three Sparkle family members just looked at each other in surprise and then looked at the one who called himself "The Doctor." The one that Princess Celestia warned them to be wary of.

"Y-You're real?" Princess Cadence said in disbelief as she looked at him. "You look like nothing more than a stallion speaking madness."

"A gentlepony speaking madness, thank you," The Doctor said with a snort. "Besides, anypony remotely interesting is mad, in some way or another." He then rubbed his chin. "Did I say that? Or did someone else say that? Wow, I really am getting old."

"Enough!" Twilight shouted as she stomped her hoof. "Doctor or no Doctor, you are coming with us, and Discord here is-"

"Coming with me," The Doctor said with a smile. "Sorry, but this fine chaotic spirit of a mad creature is now officially my patient. I'll send you the bill and the letter of recommendation for treatment later. Though for you three? My suggestion is to stop listening to brainless stupidity and listen to your reasoning for once."

"And what are you going to do about it?" Shining Armor stated as he pointed at the three of them with his hoof. "There are three of us, and you clearly have no means of defeating us."

"Oh, I'm not here to defeat you. Not yet anyway. That comes with time," The Doctor said with a shrug. "I'm actually here to escape in about three simple moves."

"Three moves?" Twilight asked.

"Yes, here is move one," He then tossed a strange green-scaled object that was round yet square on the ground. "Here is move two." The Doctor then pulled out a fuzzy pink pair of earmuffs from his coat pocket and put them on his head. He then pulled out his Sonic Screwdriver and smiled. "And here is move three."

He quickly pointed it at the object, which instantly caused a window-shattering vibration sound to echo across five streets. Everypony, including the unconscious ponies who woke up immediately, screamed and held their ears as they struggled to stay on their hooves, but their heads felt like they were being pounded with jackhammers.

The Doctor whistled and, flying down at top speed, Derpy, Fluttershy, and Flash Sentry, all wearing earmuffs, rushed out of the alley while holding a stretcher before settling down next to Discord, the only one who wasn't affected and just looked around in confusion.

"Flutters..." Discord whispered with a smile as he held his best friend's hoof.

"Hey, Dizzy," Fluttershy whispered back with an even bigger smile as she and the others put him on the stretcher and rushed around the way they came.

Twilight, gritting her teeth, attempted to follow and screamed out Fluttershy's name, who looked back and saw her former friend, but soon turned tail and continued to run until they were out of sight. Finally, the sound shortly died, and Twilight instantly rushed after them with her wings. She just managed to turn the corner when something blue disappeared, and she screamed in frustration before blasting the ground.

+}{+

"What was that?" Flash Sentry asked as he took off his own earmuffs while The Doctor concentrated on the TARDIS. "We had our ears protected, but it still felt like a ringing in my ears."

"Ice Warrior sonic grenade," The Doctor answered as he worked on the console. "Usually, those can implode your eardrums, but I lowered the intensity to make the experience like having a dreadful headache."

"Why wasn't I affected?" Discord asked as he lay on the stretcher while Dinky, Carrot Top, and Fluttershy started using first aid kids to bandage him.

"Frequency I used only affects equine type sentients. Now please hold still." The Doctor walked over with a syringe and poked Discord's arm before drawing some blood. Smiling, The Doctor walked back to the TARDIS and put the needle in a slot before typing in some calculations. "And done! Eureka! A full-on cure for the Conversion Potion that can be used on anyone!"

"Wait, what?!" Everyone but Lyra shouted in shock.

"You just made a cure for the Conversion Potion in just a few minutes?!" Dinky asked in disbelief. "That potion took Twilight and the other scientists years to create!"

"Well, technically, I've been working on it for a few weeks," The Doctor said as he continued to work without looking at everypony. "But if you think that's impressive? Wait until you see my next trick."

He then pressed a button, and Major-General Highmoore appeared from his home base on one of the screens of the TARDIS. "Major-General? Are you and your forces prepared?"

"We are, but are you sure about this?" Major-General Highmoore asked.

"Major-General, in a few hours, we will be having sake and sushi to celebrate our victory. Just tell your men to get ready!" The Major-General nodded before signing off.

"So what now? What's the plan?" Lyra asked, with excitement on her face, "What can we do to help?"

"Make yourself a cup of tea, have a few biscuits, and sit down to relax," The Doctor said with a toothy grin. "Because you're about to see a show like never before."

Author's Note

Seriously, I am glad I finally got to write The Doctor. He's one of my favorite characters of all time (When the writing is good) and I just love seeing him outwit opponents. And yes all those flashbacks are actual moments where The Doctor and various companions say their farewells to each other. Except the one with Gallus and Silverstream and Izzy, that's just to show that The Doctor has had adventures off screen. If you are wondering who my top three Doctors are its 7th (Sylvester McCoy), 3rd (Jon Pertwee), and 11th (Matt Smith)

As always, please help out at the NegotationsVerse TV Tropes Page. We even have a Regeneration Focus section: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 6

“I am the man that gives monsters nightmares. The Daleks call me the Bringer of Darkness. I am the Eighth Man Bound. I am the Champion of Life and Time. I'm the guy with two hearts. I make History better. I am the Doctor.”

The 8th Doctor

+}{+

When Princess Celestia told Twilight Sparkle about The Doctor, she was in disbelief at her mentor for the first time in her life.

She had trusted Princess Celestia to always be honest and truthful to her since she was a little filly. Her wisdom and faith allowed Twilight to do the fantastic things she never saw herself doing all those years ago when she nervously attended her classes at the Canterlot School of Gifted Unicorns. Princess Celestia believed in her destiny to change Equestria, and so Twilight believed in her teacher with all her heart.

But a time-traveling alien in a blue box? There were some things she just couldn't believe, even from her mentor. She agreed to keep an eye out for this "Doctor" pony, but even she didn't think he was that serious of a threat.

Until now, at least.

Twilight had seen many amazing things in her life, both beautiful and scary. However, she never thought she'd see a tiny police box fit an entire group of creatures, including someone twice the size of the box itself, and then disappear out of thin air. All while outwitting her with three moves and giving her the largest earache she ever had since listening to a drunk minotaur ambassador sing.

But the pain in her ears was nothing compared to what she felt in her heart.

Discord was gone, and Fluttershy with him. That meant the retrieval team had failed, and Big Macintosh was either captured or dead.

Twilight didn't even know what she would tell Applejack and her family about this. She still was hoping that Fluttershy had been brainwashed or forced into going along with Discord, but now it was clear that Fluttershy, one of her best friends, had willingly become a traitor.

Fluttershy who had been the gentlest, kindest, and sweetest of them all. Who stood by Twilight's side against their enemies even when she was terrified and wanted nothing more than to go home. The mare that told Twilight she was glad they were friends because she had never been happier in her life.

She was now Twilight's enemy.

Twilight to scream, cry, and just blast something apart, but she knew that a battle was still to be won. She would deal with her friend's betrayal later while trying to figure out what to tell the other girls. No doubt they would take it just as hard, especially Rainbow Dash.

But that wasn't the only thing that was burning rage inside her heart. More betrayal and anger were swelling inside her upon seeing Flash Sentry among those who fled with the other traitors. That opened up a can of emotions inside Twilight that she was trying hard to ignore but failing, as evident from the wisps of smoke and flames coming from her mane and tail. Royal Guards in the main camp quickly got out of the way upon seeing her return with her brother and sister-in-law as if she was a bomb ready to explode.

Twilight assumed no stallion would ever like her in a romantic sense if she was being honest with herself. Growing up, she heard all the hurtful words that echoed inside her mind while walking between the halls of class: nerdy, loser, ugly, and privileged. She knew it was because they were jealous that she was Princess Celestia's personal student, but the words still hurt. So while girls were getting really interested in boys around puberty, Twilight was more focused on learning advanced algebra, spell components, and chemical compounds.

Even after growing up and arriving in Ponyville, Twilight doubted her capabilities to find love. She had been wrong with friendship before Ponyville, and she imagined dating, something she had no experience in, would be an utter disaster. It took Twilight a long time to adjust to having friends, so the thought of having a special somepony seemed beyond reach.

And then she met Flash Sentry. One of many guards assigned to her new castle. He was trained to be her bodyguard, and their first meeting was an awkward bump where he soon helped her off the floor. When their eyes met, something clicked because they were quickly hanging out not as a princess and her guard but as friends.

He smiled warmly at her like the very dawn of Celestia's sun. He was warm, brave, strong, and somepony who could always tell who you were deep inside your heart. He tried his best to be the best and was unwavering in his beliefs about justice and honor. To Flash, Twilight was the most fantastic mare he had ever seen. Not just because of her actions, but how she did them. With friendship, love, and a dedication to helping others.

Twilight had fallen for him almost three months after meeting him, and the other girls teased her for it non-stop. She tried to argue why it couldn't work, but it all fell on deaf ears, including her own. It was impossible to deny the truth; she wanted Flash Sentry. Not just as a guard or friend, but as a lover. A soul mate. Somepony she could be one with for the rest of their lives together.

A kiss on the lips followed by a passionate night had sealed the deal, and Twilight found herself with a stallion for the first time in her entire life. They dated, made love, saw each other's family, and even protected each other through certain adventures back in their world. Her friends and family loved him, and he loved her friends and family. After so long of being together, Twilight knew that Flash Sentry was the one for her and dreamed of one day on the altar with him to seal their love forever.

But it seemed their love wasn't enough.

Flash Sentry was blinded to the fact of how badly humanity needed to be turned into ponies to save them from destruction. How could Flash Sentry not see what Princess Celestia, Luna, Cadence, herself, and so many others could see? He sympathized with them, cared for them, and urged Twilight to see his way, but she couldn't.

Humanity cannot exist as it is. It needed to change, and the only way to do that was to convert them to something that would prevent their human nature from ruining them. But while she called salvation, Flash called genocide.

That led to...the argument...and the slap.

Everything Twilight dreamed of had been ruined that day.

Flash left not just Twilight but the Royal Guard and everything behind to side with humanity. Her greatest love had become her worst enemy.

Twilight's heart had been broken in a way that could never be healed, but she would push through the sorrow and the pain to see Equestria triumphant in this war.

If it meant going through old friends and lovers then so be it.

+}{+

"Have our scouts reported anything?" Twilight asked the head of her scout division. After checking to find The Doctor and his mysterious box, they returned to their home base in the Konohana District after finding nothing.

"Sorry, Princess," a female purple pegasus in Royal Guard regalia answered with a sigh. "No sign of the traitors and no teleporting blue boxes either."

"Keep searching," Twilight ordered as she returned to the war tent where Shining Armor and Cadence were looking at the magical holographic battlefield map displayed from the crystal table.

Twilight looked at both their forces and the enemy. She saw they were still deadlocked, but the humans had started pulling artillery, rockets, and other super ranged equipment into various positions aimed at their bases, strongholds, and checkpoints.

This made no sense in Twilight's mind as she knew their magical shields could protect them easily from any bombardment. The commanding officer of this army wasn't stupid and was giving them a run for their money with several tactical displays that had impressed even her brother.

So what were they planning? Shining had stated they should attack these just in case there was a plan they weren't expecting, but they were too heavily defended by anti-aircraft guns, which were used to take out any pegasi seen in the sky.

Right now, it was merely a waiting game that allowed them to have a slight pause for the most part in the fighting. The front lines had been fighting non-stop, so Cadence ordered a halt on all forward progress to give them a chance to rest up, resupply, and replace any troops too wounded to fight or killed.

"No sign of The Doctor or his blue box thing?" Shining Armor asked, and Twilight shook her head. "How can such a small thing teleport so many creatures?"

"We can study it when we capture it," Twilight Sparkle replied as she rubbed her forehead. "Have we herded the last of the newfoals to the containment camps?"

"We just got word that they're all in and protected," Cadence replied as she sighed. "This battle is going longer than I expected."

"We can't leave until we have Discord or Fluttershy," Shining Armor stated as he put his hoof on the table. "Or at least until we know where they are. If they are beyond our reach, we can commit our forces to demolition duty on the rest of the city with constant magical attacks until this place is a giant graveyard. Until then, we need to assume they're still in Osaka."

"Have we sent a retrieval team to get the soldiers that went after Fluttershy?" Twilight Sparkle asked with a sorrowful tone. "I want to make sure Applejack has something to bury."

"That's the thing," Shining Armor said, shaking his head. "We found a few dead bodies, but not enough to make up the entire team we sent. Meaning that it's very likely they've been captured. If so, they're dead already."

That didn't make the pain in Twilight's heart lessen any better. Everypony knew what humans did to prisoners of war in their past history.

They tortured and raped or even worse things beyond imagination. Many feared such fates, but others worried that captured ponies would be turned into glue, so suicide was seen as a better alternative in many cases.

It was pretty much an accepted fact that if a pony was captured, they were considered already dead. The only disappointing thing was the inability to bring the body back, as every soldier who died in the name of Equestria was to be given a full-service funeral. It was why entire divisions of troops were trained to retrieve and teleport their dead bodies back home. Nopony was to be left behind even in death.

Applejack, I'm so sorry, Twilight thought while thinking about just how heartbroken not only her friend will be when she hears the news but also Apple Bloom, Sugar Belle, and the rest of the Apple Family.

Before they could discuss anything else, a panting earth pony guard rushed in with a panicking expression. "Your majesties! You need to come to the communication tent right away!"

"What's wrong? Is it a message from Equestria?" Princess Cadence asked with worry.

"N-No! Our communications are being jammed! All of them!"

"What?!"

+}{+

Contrary to what humans thought, ponies did have the means to talk to one another from long distances without cell phones or the internet. Instead of using electricity or satellites, they used magical-based objects. The most expensive being magical mirrors could be used to communicate if you could afford them for visual and vocal communication.

A more common method was attaching a magical link between two bonding crystals that could be used for talking, similar to a walkie-talkie. That was why, whenever Equestria landed her forces on human lands, they set up a communication tent with powerful unicorns capable of using multiple magical objects at once to mentally stay in communication with all active forces.

Only now, it seemed all those unicorns were unconscious. According to the guards protecting them, they just screamed and fell onto their back, with the medics declaring them entirely out cold. The various mirrors and crystals connected to some basic machinery were utterly out of control, with blinking flashes and swirls on their surfaces.

Shining Armor and Cadence watched as the last of the communication unicorns were being taken out by the medics while Twilight was busy trying to figure out what was wrong. "This doesn't make any sense!"

"What is it, Twilight?" Shining Armor asked as he and his wife went by Twilight's side.

"Something is jamming all the signals!" Twilight growled in frustration. "It's like there is a single powerful energy source filtering the magical connections with some kind of interference. Maybe if I increase the sound...

Twilight activated the speaker functions of one of the crystals, and music started coming out of it.

The three just blinked and looked at each other in disbelief.

"Is this...Jazz?" Shining Armor asked, eyebrow raised.

"Kinda good jazz, really," Cadence said with a shrug.

"Ugh, whatever it is, it's coming from a powerful object that's...up in the sky?" Twilight stated in surprise.

"A human satellite? But I thought we made sure to protect ourselves from them," Shining Armor said with a groan. Twilight couldn't blame him. It had been a massive pain in the butt to adjust their spells so that they could scramble any human space tech from spying on them.

"No, not that high up, but it's about three thousand feet in the air and...and..." Twilight's eyes widened.

"What?"

"... It's right over the middle of our portion of the city."

Suddenly the jazz music stopped, and one of the magical mirrors went static for a second before a face slowly appeared on it. One that the three had met not that long ago. Tapping on the glass, The Doctor seemed to be adjusting the screen before appearing before them with a smile.

"Hello there. Sorry to call in unannounced. But I wanted to ensure that your troops were confused about what to do next. Normally music like that wouldn't hurt anypony, but directly connect it to the horn of a unicorn, and it's like blasting high-powered stereos into the ears but more powerful. Hope you enjoy the soundtrack. It's a very good one."

"You?!" Twilight snarled. "How are you doing this?!"

"Oh, the TARDIS is capable of many things. Hacking into the magical frequencies of numerous communication auras is as easy as baking a pie," The Doctor said with a chuckle.

"Where are Fluttershy and Discord?" Cadence demanded.

"Oh, they're safe. Far safer with me than any of you," The Doctor said hardly before glaring at them. "They are under my protection now. As are the humans and ponies that stand against you. This planet is under my protection, and trust me, that comes with a hazardous warning label. One that you would be foalish to ignore."

"Why are you contacting us?" Twilight asked.

"I'm calling because I want to discuss the terms of your retreat."

"Retreat?!" Shining Armor asked in disbelief before growling. "You expect us to retreat when we're defeating the human forces!"

"Oh, I expect you to retreat very shortly because you're already in check, and in a few minutes, it's going to be mate," The Doctor said coldly as he moved in closer. "Here is my offer to you. And this offer comes only once, so listen well. You will cease all fighting immediately. You will take your forces and return to Equestria. You will leave behind all the newfoals as well. They don't belong to you. They belong to their families and loved ones that you took away from them. You will do this, or you will suffer defeat. It's a defeat so bad that you'll be haunted by it in your dreams to the point that not even Princess Luna can comfort you at night."

Although there was a part of Twilight's instincts that was telling her to listen to his offer, she pushed it aside and shook her head. "If you think we're going to bow to your demands, you are mistaken. Equestria has always stood against evil, and we will stand against you too."

"Evil? Oh, Twilight, you have never known real evil. Not what I've seen. I've seen things that would make the hairs of your hide turn white with terror. Races that senselessly kill out of hate, greed, and pleasure. Beings of terrible power that have eaten stars, shattered worlds, and made gods weep in fear. Terrors and nightmares of the worst emotions and feelings made manifest into flesh. And I've faced them all. Compared to them, you're nothing but children pretending to be scary monsters when you're just selfish brats who are upset nopony's listening to you, so you have to break everything to get what you want. Besides, if you want to see evil, look around you and see the chaos and death you and your people have wrought. Is this really harmony? Is this really justice? Is this salvation? No, it's nothing but that. And I will stop it. I will stop you."

The Doctor sighed. "Last chance. Retreat now. Take it or leave it."

The three leaders looked at each other for a long time before nodding in agreement. "We're not retreating."

"...Then I am so sorry for what happens next."

And with that, the Doctor ended communications.

+}{+

"Why do you have an electric guitar?" Lyra asked as she and the others sat on beanbag chairs the Doctor provided so they could sit back and watch the show. The TARDIS even offered snacks and drinks as the Doctor started plugging a few extra cables into a black and blue-styled Fender Telecaster.

"First, who doesn't have an electric guitar. They're awesome," The Doctor said with a smirk as he pressed a few buttons on the control console and upped a few dials. "Second, magic carries waves of resonance in the air whenever it's used, just like sound. If you are talented enough, you can take the same resonance of sound via an object and use it to create a means to control or neutralize the resonances of magic by manipulating the currents. Say if I wanted to negate all the shield spells that the Equestrian army is using below us, all of which are the same type, by the way, then all I would have to do is play a little Led Zeppelin."

"Huh?" Dinky asked, tilting her head.

"Basically?" The Doctor said as he got ready and grinned. "Music is the weapon."

The Doctor soon raised his hoof and crashed it down on the strings before starting to shred.

+}{+

A few seconds into playing, Unicorn ponies in the army who were tasked with holding the shields started screaming their heads off as they pressed their hooves to their horns which were glowing in various colors and sparking off like fireworks. Their non-unicorn comrades tried to help them out, but they kept pushing them away in pain while their magic started going ballistic. Telekinesis, plasma blasts, bolts of lighting, fire waves, water gushers, and more were being cast rapidly from the unicorns, who were yelling as if their heads were cracked open.

Above the various grounds, territory, and bases the Equestrian Army had under their control from their conquest of the city were the numerous magical shields that had protected them from any outside harm. They stood proud in shiny purple colors, with not even bullets able to get into their protective domes.

However, just like an egg being hit with a spoon, cracks suddenly began to appear. Small ones at first, but soon larger ones appeared. Those who looked up gasped in horror as their defensive barriers were being broken.

Commanders tried to get the shield using unicorns to concentrate and fix the cracks, but they were in too much agony to respond. Other unicorns, including backup shield maintainers, tried to assist but soon joined the screaming crowd. When asked what was going on, one of them screamed,

"It's like a thousand angry voices in my head! Make it stop!"

Word quickly spread to the royal family as all three watched in horror as even the shield under them started to crack. Shining Armor, having mastered shield magic as a personal talent, tried to assist, but he too fell down, gasping in pain while holding his head. Cadence was right there by his side as he winced and tried to stand up. "It's like...something is interfering with the magic...something...heavy...loud...and painful."

"The Doctor must be doing something! We have to reinforce the shields!" Twilight shouted, but it was too late.

Unable to take anymore, many unicorns finally ended the spells, allowing silence to flow into their heads once more, while others outright fainted from the pain. The various shields all over the Equestrian territory began to shatter. The ponies watched in horror as their protection evaporated into bits and pieces that soon disappeared into the aether. They were completely exposed to attack for the first time since the battle began.

+}{+

"Sir! Their shields are down!" A UN HQ watcher reported. The room was silent for a split second as multiple others confirmed the report.

"How many of them are down?!" Major-General Marshall Highmoor asked with hope in his heart.

"All of them! All of them are exposed!" The watcher responded with awe.

Grinning, Major-General Marshall Highmoor got his com and quickly ordered the communications officer to address all forces. "This is Major-General Highmoor! The Equestrians are exposed! I repeat, the Equestrians are exposed! All ranged forces are to hit them with everything we got! The targets issued to you will be hit with non-stop bombardment! Not one shell or missile is to hit the containment camps! Now send them all to Hell!"

"YEAH!"

+}{+

For a few seconds, upon seeing the last of the shields fall, there was nothing but blissful silence. And then, like the mythical dragons of Japanese lore, there were roars. There were endless roars of high-powered artillery cannons, missile launchers, and mortars unleashed in a barrage of righteous fury.

The front lines of the Equestrian ground forces were front and center to the bombardments that rained down on them like grenades from rainclouds. L16 81mm Mortars, M120s, and M224s were like organ pipes singing a death tune upon the stunned and confused front lines that were soon screaming.

Lost limbs were scattered into the air, entire streets of soldiers were wiped out, and field equipment, arrogantly thought protected without needing any cover, was destroyed in a wave of motor fire. Once their front was significantly damaged, the human forces of the U.N. and J.S.D.F charged forward with renewed spirit, followed by their armor and vehicle divisions.

Dazed, wounded, and confused, the Equestrian front forces stood no chance as they started getting slaughtered and pushed back beyond their borders.

Further on, more dangerous ranged guns were howling their vengeance across the city. M777 gun-howitzers and FH-70 towed howitzers were firing upon enemy camps and occupied buildings, crumbling the establishments into dust.

Casualties were beginning to rise higher than any thought possible in this fight as the panic started to set in that they were completely exposed. In their belief that their magic shields were untouchable, there was no additional cover to protect them from attacks from long range or in the air. Everything had been grouped together, with entire platoons and divisions forced to take whatever cover they could get before they were utterly wiped out.

But this wasn't just enough, thanks to the M142 salvo rocket systems that were going even farther and preventing any retreating force from making it out without multiple casualties.

Even the furthest of the territories under pony control were attacked by missiles that obliterated anything in their path. One would think they were spears from heaven as they descended on the ponies from numerous M270 salvo rocket systems and M270 MLRS. The only places that had not been targeted were the main camps holding the leadership of their army and the most distant of bases near the bay. From the human side, it was like seeing hope rising from the smoke and fire, but for the ponies of Equestria, it was like seeing doom upon the horizon.

+}{+

"Woah," everypony in the Doctor's TARDIS whispered as they saw the chaos below. The Doctor turned his guitar off and placed it aside before turning to the TARDIS controls.

"That's how you bring down the house," He said as he started spinning a wheel before pressing a button. "And for my next trick? We make a little rain."

+}{+

From outside the TARDIS, a small hole opened up on the top, and something quickly shouted out of it. It sailed upward for about fifty miles before exploding and spreading a large cloud of dust around. For about six minutes, nothing happened. Then the clouds started to change color. They turned darker before beginning to rumble. Forming up together, faster than thought possible, the large clouds began to rain down below on the city and spread until every corner of the area was getting wet.

+}{+

Twilight, Cadence, and Shining Armor watched in horror on the holographic map showing not just the loss of territory with each passing minute but the number of casualties that had reached the highest casualty rate for the Equestrian army in any single battle. Their perfect defense crumbled like a sandcastle against a tidal wave.

Sorrow filled their hearts at the thought of their fellow ponies being slaughtered in a seemingly endless barrage of counter-fire. Numerous officers were running around outside, trying to organize multiple retreats to back up bases (what was left of them) or offer ideas of counterattacks, but with the seemingly endless waves of artillery fire from a distance, it was unlikely that they were going to amount to anything so quickly. Especially since the entire human force was moving like a tsunami across the city.

“This is a disaster,” Shining Armor whispered in frightened awe before getting his act together. “We need to send an order to all front and middle divisions to retreat to the backup line. Abandoned the main line and secondary line. Leave any wounded behind.”

“Leave the wounded?!” Twilight asked in horror.

“They’re sitting ducks, Twilight!” Shining Armor growled. “If we’re going to turn this around, we need to-”

“How are we going to turn this around?! Our defenses are practically gone!” Shining’s wife shouted in disbelief.

“Your majesties!” One of the guards shouted in haste as he rushed in.

“What?!” Shining Armor shouted with fury.

“The...the...the newfoals!” The guard shouted while catching his breath.

“Oh, great, what about them now?!” Shining Armor groaned.

“They’re...they’re...turning back into humans!”

Twilight instantly shouted with the Royal Canterlot Voice so loud that even the artillery barrage distance couldn’t match her volume.

“WHAT?!”

+}{+

"By the Princesses, look at that! I've never seen so much damage!" One of the guards in the containment camps shouted from inside the steel fence barrier used to herd the newfoals together. They had been watching the battle from their location and feared the worst when the shields fell. But to their surprise, the big human guns did not target them once.

This led them to keep their focus on trying to calm the newfoals. They were all scared and asked various questions in confusion. The guards had to assure them that everything would be okay, but some seriously considered just ditching them.

It was always a chore having to guard newfoals. Whenever newfoals transformed weren't that bright at first and acted so confused and clueless until they could be adequately reeducated back in Equestria. Australia had become their main ground for keeping them so they could be fitted for Equestrian society, and some guards couldn't wait to go back there to drop them off and head for the beaches.

"I didn't know it was going to rain today," One of the other guards asked as they looked up at the water droplets falling down on them.

"Well, this is great. Not only are we getting attacked with our shields down, but we're going to catch colds as well," The other guard sighed. "Might as well bring the newfoals in before they catch a-"

Suddenly, bright lights were emitting from the center of the containment camp where the newfoals were all located. The guards all raised their hooves and gasped upon seeing the shining glows. "W-What is this?! Where is this light coming from?!"

"The...The newfoals!" One shouted with narrowed eyes as every newfoal was shining bright.

Slowly, the forms of the glowing white newfoals began to reshape. Growing taller and thinner while no longer standing on all four legs and now just two. Each of them was transforming before the very eyes of the guards, who soon lowered their hooves in awe. Then, as the light began to die, that awe was replaced by shock, disbelief, and horror.

Opening their eyes, the former newfoals looked around and then at themselves before seeing no hooves but hands and feet. No manes, save for the hair on their heads and faces. They had skin and clothing instead of furs. No wings, horns, tails, or even Cutie Marks.

They were, once again, human.

There was a long stunned silence between the humans and the ponies until both groups realized something. Because newfoals were practically incapable of committing violence, the guards were left with a skeleton staff and very few weapons. Seeing as they were so deep in their occupied territory in the city, they thought it was impossible to be attacked. There were so many humans in front of them that they practically made an army. And all of them soon held expressions of pure anger.

These gaijins had come to their city, their nation, and attacked it. They destroyed countless centuries of historical monuments and buildings, killed their people, burned their temples, and ravaged their soil with blood and lies. Worse, they had taken them from their once-proud human bodies and turned them into abominations.

There was only one thing to do to correct this injustice.

"天皇陛下万歳!" One man shouted, and, upon hearing this, the entire camp of the Japanese people charged forward as the ponies screamed in horror.

It was like this in all the containment camps as newfoals turned back into a raging force, humans who showed no mercy to their captors even as they begged for it.

The spirit of the rising sun had awakened once again.

+}{+

"This is impossible! Impossible!" Twilight shouted as she ranged back and forth, her hair spiking out in a panic. "It took us years to make that potion! Years! There is no cure! Even if there was, making one wouldn't take so quickly! How is that even possible?! How did he get past the enzyme?! What chemical formula is he using?! How is he even distributing it at such a high rate?!"

"Twilight!" Cadence shouted as she grabbed her sister-in-law and shook her to calm down. "We can worry about this cure later! We can't stay here! We need to retreat!"

Twilight looked at her foalsitter before looking at her brother, who looked reluctant to say anything, but with a heavy heart, he nodded. "Cadence is right. This battle is lost. We need to order an emergency retreat as soon as possible."

Twilight bit her lip and closed her eyes to fight the tears before nodding as Shining Armor gave orders. Sitting on her haunches, she lowered her head in shame, knowing that she would be returning to Equestria with the first absolute defeat on her shoulders in hundreds of years.

What would her friends think?

Her subjects?

Princess Celestia?

How could she look into the eyes of the families of the soldiers that died here and tell them it was all for nothing? Twilight had never felt more helpless and was doing everything she could to prevent herself from tearing up. Cadence seemed to sense this and slowly wrapped her forelegs and wings around Twilight, comforting her.

All Twilight could only wonder was how this could have happened? They had everything going for them. The initiative. The tactics. The forces. How could everything have gone so far down in such a sudden twist of fate? There was only one answer. One dreadful answer that made her shiver.

Twilight had faced beings like Nightmare Moon, Discord, Queen Chrysalis, and Tirek.

But never did any of them feel like what she felt when she realized that The Doctor would be the greatest enemy she would ever face. Doctor...I swear I will stop you...

However, before any other action could be taken, there was a sound of a dozen angry figures in the air buzzing around with dread filling in everypony's stomach. They saw what appeared to be angels of death sailing far above them, but any military expert could tell you those were just planes. Bomber planes. A combination of US Northrop B-2 Spirits and Russian Tupolev Tu-160s. All of which were sailing above and releasing their payloads.

The reinforcements that Osaka had been waiting for had arrived.

"EVERYPONY, TAKE COVER!"

And in a second, there was a sea of fire.

+}{+

It took two hours for human forces to finally reclaim everything lost. The entire south and west side of Osaka had been utterly ruined in the counterattack. Buildings were destroyed, roads were upheaved, and corpses were everywhere, primarily ponies.

What Equestrian survivors were lucky to find shelter, or surrender upon failing to join in the emergency teleport, had been taken as prisoners of war. Yet, despite the ruin and destruction that lay before them, the humans were all celebrating. For two years throughout the war, there had been defeats, stalemates, and bittersweet victories for humanity.

There was a true victory at long last, here in Osaka, Japan.

A victory that proved that Equestria could be defeated. A victory that proved that humanity was strong and could prevail. Word was already spreading throughout the internet and news as pictures, videos, and tik-toks were trending, showing various rising hashtags as citizens, soldiers, and survivors all came together to show that they had achieved the impossible.

They had won.

And throughout the cries of victory and celebrations, a cry shouted out to the heavens.

“Osaka Stands! Banzai! Osaka Stands! Banzai!”

Lyra, watching the celebrations from the TARDIS, looked over at the Doctor, who was watching beside her. Discord had been taken away for medical treatment with Fluttershy accompanying him while Derpy, Dinky, Carrot Top, and Flash had all joined in the partying. Looking over at his companion, The Doctor smirked and asked, "Still feel like we could be doing more?"

"Heh," Lyra chuckled before smiling warmly at him. "You did it. You actually did it. You not only gave Equestria its first real defeat, but you managed to create a means to turn newfoals back into humans. This...this is a miracle."

"First off, we all did it," The Doctor said with a smirk. "All of us did this together. Even you."

"I didn't do anything special," Lyra whispered with a sigh. "Compared to everypony else, what have I done?"

"You stood for what was right," The Doctor said with a warm smile as he patted her on the back. "You were the first to realize what was wrong with what Equestria was doing. You stood up and said no when others were too afraid to do so. All it takes is one pony to stand up and say no more to start a chain of events that will lead to something amazing. This is what you helped accomplish. Your voice, determination, and courage matter because you did the most important thing needed. You told the truth. A truth that needed to be heard to fix what was wrong."

Lyra grinned and hugged him. "You know how to make a mare feel special."

"Well, I have a way with mares, stallions, and all other genders, both Equestrian and alien," The Doctor said with a chuckle before frowning. "However, we've not ended the war. Merely won a battle. Now that Equestria has tasted this kind of defeat, things will only escalate."

"How bad will things get?" Lyra asked, tilting her head.

"Well, desperate ponies will do desperate things..." The Doctor said but soon clapped his hooves and smiled. "But that's for tomorrow. Today we celebrate. Shall we?"

"Go get some of that sake, and let's party, Doc."

+}{+

Disaster.

A complete disaster.

That was all Celestia could think of as she stood in the Emergency Waiting Room at Canterlot General Hospital.

Less than five hours ago, The Kingdom of Equestria had had its worst defeat in the war and the worst defeat in nearly three hundred years.

Only 32% of the Osaka Invasion Force had returned, with more than half of them wounded or crippled for life. Everypony else was either dead or captured. What's worse, if the reports were accurate, the humans had found a way to reverse the Conversion Potion. The ESS had already shown her proof that humanity had a counter to one of their greatest weapons, which had sent Princess Celestia into a state of total fear. Combined with the failure to capture Fluttershy or kill Discord, this was a complete failure of epic proportions.

And she knew who to blame.

The Doctor.

He had done this.

Cadence had all but confirmed it.

He protected Fluttershy and Discord, bypassed their magic, crippled their unicorns, allowed the humans to bombard them to near oblivion, cured the newfoals, and sent Equestria into retreat without anything to show for it. All in a few hours.

Princess Celestia feared what he could do in a week.

There was no way to prevent this news from spreading; no doubt her subjects would panic in horror and ask questions. There would have to be an official statement from the crown to address this issue, but this was the furthest thing Celestia had on her mind. Right now, Twilight and Shining Armor are her focus.

The Princess of the Sun had no idea how long she had been standing still with a stone face of worry with Luna by her side, doing her best to comfort her big sister, but it felt like an eternity as she waited for news of the siblings' treatments.

The bombardment had severely wounded them, with Shining Armor getting the worst of it thanks to Twilight's alicorn biology protecting her better than the average pony. Princess Cadence had practically carried her husband and sister-in-law to the emergency teleport glyphs while still issuing orders. Still, it was clear from her bloodshot eyes, dried tear mark cheeks, and terrified expression that she was this close to a freakout.

She wasn't the only one. Twilight and Shining's parents held each other in near-endless sobs while Twilight's friends reacted as expected.

Rainbow Dash was pacing around, looking ready to break something.

Rarity was sobbing into tissues.

Applejack had her head lowered and was saying nothing.

Pinkie Pie was staring at the floor with her mane completely down and her wide eyes watering.

And Spike?

He had threatened the entire hospital staff that he would burn the building if they didn't save his siblings. The only one of their family not here was Flurry Heart, who Cadence refused to have here out of fear of seeing the state her father was in.

Finally, the doors opened as everypony stood up, waiting for a blood-covered unicorn doctor (one that Princess Celestia personally trusted) to make his way to them. "Family of Princess Twilight Sparkle and Prince-Consort Shining Armor?"

"Are they okay, Doctor Wellhoof?" Princess Celestia asked, stepping forward with fear in her tone.

"Princess Twilight is going to make it," Doctor Wellhoof replied, making more than one pony sigh in relief. "However, we had to amputate one of her wings, and her left eye was too damaged to keep in. She'll have to wear a patch over it for the rest of her life or get it filled with an artificial replacement."

"And Shining?" Cadence asked desperately while the doctor just stood there in silence. "What about my husband?!"

"...Halfway through his surgery, Prince Shining Armor's heart stopped. We tried to resuscitate him, but we couldn't. I'm sorry, but he's gone."

Author's Note

Loved writing this part. As always, please help out at the NegotationsVerse TV Tropes Page. We even have a Regeneration Focus section: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 7

“Everything’s got to end sometime. Otherwise, nothing would ever get started.”

The 11th Doctor

+}{+

It had been two weeks since the Defeat At Osaka as many were calling it.

All of Equestria had been horrified and in mourning over the loss of so many of her brave soldiers that perished or were captured by the humans.

Cities and towns held vigils at their local Churches of Harmony as masses went on for hours in prayer to the holy alicorns to deliver the souls of the lost to Elyisum, and avenge those that had died. The families of those who had lost relatives to the battle were cared for both by their government and their local communities, but nothing would bring back their lost loved ones.

The survivors of the battle told their stories with bitter tears and hatred in their tones.

They talked about how the humans brutally destroyed their lines, rushed them without mercy, and saw their comrades die in horrible ways from being shot to death to one J.S.D.F. commander using a sword to slice a unicorn’s head off.

Many couldn’t sleep as they kept fearing the explosions of the artiliary or bombs of the human army coming to get them at any time. Others suffered mental and emotional breakdowns and had to be committed. One or two just killed themselves with notes stating how they couldn’t take the nightmares anymore.

Outside of the grieving, there was disbelief.

Never before had any Equestrian thought that their mighty forces would suffer a defeat so badly. The last time they had ever lost such a battle with high casualties had been the Battle of Westbeak in the griffin lands during the Fourth Pony-Griffin War three hundred years ago. It was often said that the battle had been what caused the war to become a stalemate slightly in Equestira’s favor rather than a full on victory. Not that it meant much to the griffins as their kingdom at the time fell twenty years later due to rebellion before falling into another warring states period.

While there had been rough battles in the Conversion War, most of them had been victories or stalemates.

This was the first full on defeat and many couldn’t wrap their heads around that. Even the fact the Osaka invasion force had Commander-General Shining Armor and two alicorn princesses and still lost was mind blowing.

It made ponies fear that the war wasn’t going to be as quick as they thought as they knew the humans would use this victory as a means to continue fighting with renewed vigor. All future invasions were put on hold for the time being and all Equestrian owned territory was put on full alert.

Rumors that traitors had been behind the downfall spread and the E.S.S. was working over time as ponies started accusing anypony around them of being spies or harboring traitorous thoughts.

It didn’t help that it finally became publicly known that Fluttershy and Discord had become traitors.

It broke the hearts of many, including foals, that one of their heroes had betrayed them to the point that any memories of her that old friends and family had were thrown out.

The Church of Harmony even declared her soul was doomed to Tartarus upon her inevitable death at the hands of the Princesses who would avenge their fallen.

There were also rumors of someone called “The Doctor”, but the E.S.S. stated that such a being wasn’t real and nothing but false propaganda.

Most had to agree with that. A time traveling alien in a blue box? Absurd.

If there was one positive thing that the defeat had done it was drive up recruitment. Seeing their brave fathers, mothers, sons, and daughters buried to sleep forever more, had invigorated many to join up to avenge them. Their pride was on the line and the safety of Equestria was paramount with many hoping the Princesses would have plans for a counter attack to see justice was done.

However, the Royal Family was more concerned about the wake and funeral of Commander-General Shining Armor.

It had been agreed upon, by both the crown and family, to have the wake and viewing ceremony in Canterlot before having the body taken to the Crystal Empire for the official funeral and burial into the catacombs of the past rulers of the nation. For as much as he was the Prince-Consort of the Crystal Empire, Shining Armor had been born and raised in Canterlot.

The least the city he loved so much could do was say farewell to him.

The third day of the five day viewing wake had been the same as the other two days. Prince-Consort Shining Armor had been placed on a purple pillowed silver-white casket, decorated in the finest of jewelry and cloths, in the middle of the Grand Cathedral of The Sun and Moon, the holiest place in the Church of Harmony faith.

He lay inside the lidless casket, void of any and all wounds to the point that it would appear he had been undamaged at all. Yet the shrapnel in his chest had done him in from the bombing. In his will, he asked to be buried in his Grandfather’s uniform and wore it with pride even in death with his hooves gently placed above his stomach as his expression was one of utter peace. It had been Cadence's request that he was smiling in death because it was his smile that she and Flurry Heart loved so much about him.

Numerous flowers surrounded the casket to the point that they made a near field of themselves save for a small circle for walking around the casket to pay respects. The lines of which extended so far out they went down to the lower levels of the city.

Guards wore black armor with purple and white sashes in honor of their beloved Commander, with many unable to keep themselves from crying even as they stood vigil over his body. Near the altar of the Church was the family, dressed in mourning, who stood there watching the lines of mourners move as funeral music played constantly around them.

Princess Celestia had seen friends die before, but that didn’t make it easier when it happened.

Shining Armor had been more than just a friend, he had been family.

Loyal. Protective. And brave.

Equestria was a darker place without him.

She glanced at Luna whose expression was one of anger and rage. It had taken all of Celestia’s willpower to force her younger sister to hold back on unleashing everything she had upon Osaka herself to the point where she wanted to make the atomic bombings Japan had gone through look tame in comparison.

Celestia was able to get her to calm down by pointing out that not only was humanity riding high and confident with their latest win, but they still had no means of defeating The Doctor. Plus, this was a time when family needed to come together. Luna conceded this but demanded that, come the next invasion, she would personally lead it herself.

Twilight Velvet and Nightlight were still in tears upon losing their son. Princess Celestia swore that she would take care of them for the rest of their lives. Anything they wanted was hers to give. She even made it so they never needed to pay for anything, yet that would be of no comfort for the fact they lost their son.

Meanwhile, Twilight, her beloved student, was standing there with a cold and stoic expression while her one eye was focused on her brother’s corpse while the other was behind a black eye-patch.

Something had changed inside Twilight after the battle. She had become colder, methodical, and spoke less to anyone save except for important factors like the war or planning her brother’s funeral. None of her friends, or even Spike, could get her to talk much. Princess Celestia even tried to get her to talk but she said that she couldn’t think of anything except one thing: Destroy The Doctor.

The fact that The Doctor had played a role in killing her brother and crippling her to using only one wing and eye for the rest of her life was bad, but reversing the Conversion Potion? The most prized alchemical achievement in modern history that took Twilight, Celestia, and dozens of other scientists to make? That was just applying oil to the burn.

Princess Celestia still couldn’t believe such a thing had been done, but it was true. Humanity had applied the cure The Doctor had created (without mentioning him personally for some reason) to all the newfoals that they had in their borders. Princess Celestia personally saw over a hundred videos of newfoals turning into humans again before she was forced to accept that this was the truth. One of their greatest weapons was now null and void.

The newfoals in their borders were restless when this was revealed. They claimed they didn’t want to be humans again and even started asking their fellow ponies to kill them if this happened. Another headache that Celestia had to deal with.

The other person who had been in complete despair was Shining’s wife, Cadence.

Although she was not crying, her eyes told a different story. When Celestia agreed to take Cadence in as part of her family by formally adopting her, she had always been so full of love and life in her expression that she was her own ray of sunshine. Cadence had quickly worked her way into Celestia’s heart and she showed herself to be wise, talented, and caring. A perfect ruler to work with Twilight when she and Luna passed the crown to them one day.

Now, that once happy alicorn that could brighten any room was in utter despair. Cadence had cried non-stop for days to the point that she couldn’t do anything with helping with the funeral save for one or two things.

She just didn’t have the energy in her to do anything as any time she looked at Shining she looked ready to collapse in grief. She couldn’t even make the opening speech on the first day of the wake.

The only time she ever snapped out of her funk was when she had to take care of Flurry Heart, who was a mess in herself. She only looked at her father for a few minutes on the first day of the wake before teleporting away in sorrow. Locking herself inside her room, she refused to come out and only let Cadence, Twilight, and Spike inside to talk or comfort her.

Currently, she was still inside her room sobbing her eyes out while Spike was with her to be there.

And all of it was his fault.

The Doctor.

Ţ̸̡̩̰̙͎̬̱̼̺͂̐̿͘͜ḩ̵̛̫̤͔̱̼̤͍̳̰̘̰͆̓̽̊̄̀̓͊͜ë̵̪̰̗̰̗͓̰̝͕͍͍̺̭́̉̿̿ ̴̙̂̓̌̏̌͝D̸̨̀̀̄͌͂̉̿̈́͌̈́̇͒̈́͜ơ̴̲̲̗͚͙̳̑͆̾͂̀̿̽̌̓͂̌́̀͊c̷̭̬̖̺̠̠͍̖̀̍̄́͊͊̇̍͝t̸̡̜͖͚̲̯̤̙̤̜͉̖̗̍̍́̌̓͋̄͋͊̌̀͜͝͝o̶̧̦̘͈̩͎̮̥̣͍̲̥̖͌̆̂̏́̊̃̚̕r̸͕̪͓̺̮̜̯̺̖̬̟̋͌̅̿̌̾͑̾ ̷̧̢̥͔̩̫͚̹̬̲̣̄̊̊̿̆͗͘͠î̸̦͉̲̙͐̈̏̚ŝ̸͔̻͈̓̄͊͝͝͠ ̴͉̫͊͊ǫ̴̺͊ū̵̡̮̋ṙ̵͇̙͔͚̅̿̓̓ ̴̙̻̯̝̯̮͙͍̐̓̿̑̽͒̓̾͜͜ͅè̴̥͕̮͇̎n̸̨͔̰̐͂̆͆̇͗͊͐̍̇̆́̈́̇̊e̶̺͖͕̘̦̱̓̋̅̅̀͛̌̉̐͊̃͒̎̚m̸̢̢̯͉̳͎̘͍͍̈̑̐͊̀̉͋͌̍͘͜ͅÿ̶̧̛̖̤̲̱͕́̉͊͛̐̌̔̈͠͝ ̵̹̄̎̈́̃̆͠a̸̧̦̝̮͆͊͂̒̈͒̓̏̚n̸͓̥̠̬̠͚̉͂̈̈d̸̳͔̩̩̮̤͔̻̟͙̻̀͗̍̓͌̆̊̂̇̊͜ ̵̡͖̯̰̮̮͎̙̹͙̠̥͎̅͑̚ḩ̶̯̪̞͇͔̼̄̒̈́̇͂̅́̂̉̓͑̀͠͝ę̴͇̠̰̩͙̼̟̠͒͒͐̄̇͝ ̵̧̺̣͇̬̣͙̲̦̄̅̇͘m̸̢̬͓̘͔͉͔͓̜̳̪̝̣̮̺̄͒̐͋̾͛͑̂̄̕͠͝ṷ̷̧͓̩͖͗̈́̃̔̂̃̔̅̓̄̌͘̚͜͜͝s̶͈̜̭̖̩̲̦̫̔͑̓t̴̡̰͈̱͎̀̈́̄͆̓̽ ̴͎̪̠̥̳̙̠̝̘̱͔͎͕̺̉̉̒́̓̆̀̀̌͋̈́̈̂̔b̵̛̩̄̌̐̃͗́̈́̓͠͝e̸̛͖̞͎̬̝̗̔̏͆̀̉̓͌̒̿̎̈̽̕̚ ̵̢̮͇͚͉͕̤͍͔̠̫̳͕̈́͊̊͒d̷͍͓̗̮͚͕̮̅̎̏̽̎̌͛̓̽͆͊́ę̴̡̼̗͖̦̤̬͖̰̼̿̆͌͆̑̔͑̓̍̍͊͘͠͝͝s̷̢͉̗̪̮̪̲̻̟̞̙̋͐͝ͅṱ̶̱̳̫͚͎̞̪̇r̸̲̞̦̙̈́̓̌̋̆o̵̦̹̻̞̬̲͓͐̌̇̓͝y̶̛͙̘̙̙̐̒͑̽̎̀͘e̵̻̗͓̬͚̎͆͛̓̐̏̽͒̆̒d̶͍̺͓̦̖̦͌͑͛̔͛͛͛̂͆̈́̐̐̕.̴̡͍͎͚͈̼̤̖̰͔̗̪̊̈́͊ͅͅ

“The Doctor is our enemy and must be destroyed...” Celestia whispered.

“Did you say something, Sister?” Luna asked.

“Hmm?” Celestia blinked before shaking her head while wondering what she just felt, but dismissed it. “No, sorry. I was thinking.”

The wake continued as Princess Celestia slowly closed her eyes to calm herself and let the funeral music playing on the speakers continue. That was until they suddenly stopped and static began playing instead. Opening her eyes, Princess Celestia glanced at the speakers as the nearby technician crews tried to quickly fix what was going on much to their embarrassment as everypony stared at them awkwardly.

However, they all soon froze when the static ended and there was silence to replace it before...

“Citizens of Equestria. This is Lyra Heartstrings talking to you from Geneva in Switzerland.”

Princess Celestia felt her jaw drop and she was sure she wasn’t the only one. Everypony had frozen in place as the words of the infamous traitorous pony that had been wanted for months were now speaking to them. Before anypony could even begin to question how, Lyra continued.

“If you are wondering how I am speaking to you on your radios, speakers, magic mirrors, telecommunication crystals, and what few human electronic devices I know some of you are keeping in secret, this broadcast has been designed to hack into every form of communication in Equestria so that everypony can listen. So you can hear something that neither the Equestrian Secret Service or Princess Celestia and her cronies want you to hear. And that is the truth.

The truth about this war. Why we came to this world. And the horrors that we have partaken unknowingly thanks to the actions of a madmare. I know that most of you are going to be told this is a lie and that you should stop listening to me. That you should continue to listen to your precious ‘goddesses’ and ignore my heretical words. But you will listen because it's time you open your eyes.”

Twelve years ago, we were told we were coming to this world to save it from destruction. That the human race needed guidance to save them from extinction.

This was a lie.

The intention of Equestria was always to convert humanity into ponies, even before we knew of the barrier and its deadileness.

Princess Celestia had already given up on humanity even before we came here and assumed they were beyond saving so she decided on two options: Assimilation or Annihilation.

She chose to play god to a race that she had no right to control or decide for. A race that, while guilty of many faults, has achieved much in their time here on this planet. A race that is not too different from us and our past. We ignored most of our history before the unification of the tribes and the building of Equestria, but did you know that this is not the first time in our history that our tribes have been united?”

Whispers were uttered in confusion as Princess Celestia’s eyes widened. How...how does she...of course, The Doctor.

“The Empire of Ponita.

The Empire of Alicornia.

The Confederacy of Coltabana.

The Union of United Equines.

These were all nations that once held multiple pony races—some that no longer exist—that worked together in harmony for years before their downfall through war, hatred, and mutual destruction.

The Great Ancient War, which we only know very little about, turned out to be the one that divided us and set us back on a technological scale beyond counting. The three tribes blamed each other and set aside the hatred that lasted for three hundred years until we were united again.

Why is this not known?

Because Princess Celestia and Luna deemed it better that we remain ignorant of our past in fear of repeating it.

If so, they did a poor job. Because one of the things the Empire of Alicornia did was try to take over other races to enslave them until they revolted. The Union of United Equines made super powered magical weapons against the Holy Dragon Empire and ultimately they destroyed each other with them. Sound familiar? Because it’s very similar to human history. The history of many other species back home. The truth is that all life follows a similar history and that no race is an exception from the other. Not even us.”

“How does she know of this? We made sure to burn all the records!” Luna hissed to Celestia in secret.

“The Doctor must have known. Remember, he can apparently travel through time itself. I wouldn’t be surprised if he was there,” Celestia hissed back.

“We always were taught that Equestria was the first time we were all united together, but this was a lie. We’ve united, fallen, and repeated this process many times over. Does that sound like some chosen race to you? Or every other race in our world? Or even humanity?

In the end, our history is no different from their own. Only they choose to embrace their mistakes, learn from them and try to do better even if they don’t succeed. We just cover our ears, eyes, and repeat to ourselves ‘it's not real’ out of forced ignorance.”

There was a brief silence as everyone waited for Lyra to continue.

+}{+

Listening in from their shared radio, Vinyl Scratch and Octavia Melody, roommates and best friends, were listening to the broadcast as well. While Vinyl had always been against the war herself, being a mare of peace, she and Octavia, who disagreed with her, never let their feelings come between their friendship. Vinyl looked at Octavia who was looking at the radio with interest and wondered if she was going to finally convince her friend that she was right.

“We are repeating the mistakes of our past. We are letting hatred and fear guide us. We are taking over a world that not only doesn’t belong to us, but killing a race.

Yes, killing them.

Converting them into mindless drones who just do nothing but love Equestrian society and hate everything else.

Have you ever talked to the newfoals? Listen to them speak? They are like robots that are programmed to obey us like slaves. They cannot refuse to deny any service asked by any Equestrian because they are brainwashed to do so. They will not even refuse sex because they cannot mentally say no. What does that sound like to you?”

“Oh my gosh...” Octavia whispered in horror as she covered her mouth while Vinyl just stared at her in confusion. Swallowing what was in her throat, Octavia said, “One of my fellow cello players...he told him his cousin has been sleeping with this newfoal and...one time when he joked about having sex in public, she thought he was serious. What if...what if...”

Vinyl grit her teeth and turned back to the radio.

“We don’t let the newfoals keep their culture because we are determined to wipe it out. All the art, statues, books, music, theaters, movies, and more. All the creative works of humanity are being destroyed. Its wonders burned. Its soul is being sucked dry until nothing remains. We are killing them in every manner possible. Not just through physical violence and forced conversion, but by erasing their very spirit.”

At that moment, Vinyl made up her mind. To hell with Equestria. To hell with the princesses. How could she call herself a musician if she was going to let this happen? She glanced at Octavia’s firm expression and Vinyl realized she wouldn’t be fighting alone. She would be fighting with her best friend at this too.

+}{+

“This war we are fighting is a needless war.

We attacked first because it was our holy duty to force humanity to convert to us.

That they were beyond saving.

The Princesses are not gods. I don’t know if there is a god or not, but I know that any loving god would not want their followers to kill others just for disagreeing with them. And if his followers did, that god would never accept them into whatever afterlife awaits them.

We believe the Princesses to be gods only because we were taught that our entire lives, but if they are real goddesses then why do they always need other ponies to fix their messes like Discord, Nightmare Moon, Tirek and so forth?

Why not revive the dead such as those who have fallen?

How can they bless those entering the afterlife if they are here with us on the mortal plane?

Moving the sun and the moon is the only reason we use as an excuse for their so-called ‘divinity’ but unicorns were doing this before them.

And before them the sun and moon were moved by the kitsune and lycans respectively.

Before them were the dragons.

And even before that they moved on their own.

If they really are a duo of powerful sun and moon goddesses, why not use this universe’s moon and sun as weapons to manipulate the weather to wipe out humanity? They cannot. Because they aren’t as powerful as you might think. Especially if they can easily fall to a Changeling Queen, an evil centaur, a Spirit of Chaos, or even a bunch of sharp thorny vines while letting a bunch of non-divine ponies stop them.”

“Father, are you sure we should be listening to such heresy?!”

“...Just be quiet, Halberd. I want to hear this.”

“Because of our full devotion and blind loyalty to the Princesses, or alicorns in general, we have forgotten to think for ourselves.

Think about the humans you interacted with, the technology they showed, the wonders you saw, and what you learned from them.

Was all of it really evil?

Wasn’t some of it good?

Did you not enjoy the feeling of riding an airplane?

Taking in the wonders of their national parks?

Love their shows and movies?

Listened to their music?

Get healed by their advanced medicine and healthcare?

They were able to connect with each other with information free for everyone to share.

They can go to space. They can create alternate forms of energy we never dreamed of. All without magic!

They have advanced factories, inventions, methods of distribution, philosophies we never thought of, and more.

The only reason they sound like a barbaric nation is because of how they wage war. Yet look at what we’ve done in this war? Aren’t we barbaric then? Or is it because of the so called “Elements” that we value so much that make us different?

Well, I’ll tell you right now. Equestria failed to live up to those Elements.”

+}{+

“WHAT?!” Rainbow Dash shouted as she listened in with her fellow Wonderbolts at their HQ. She was about to get out of her uniform and head to the wake to meet up with the others when Soarin came in with the radio playing Lyra’s speech. “What the buck does she know?! She’s a disloyal bitch!”

“We failed at Honestly because we’ve lied not just to the human race, but to ourselves why we are here. Not to mention the propaganda you hear is nothing but horse dung.

We failed at Generosity because instead of offering magical means of helping humanity we’re using our magic to hurt them and convert them. All without their free will.

We failed at Laughter because we’ve caused untold amounts of deaths, suffering, sorrow, sadness, and pain.

We failed at Kindness because we assume the worst of humanity and make them suffer at seeing their cities ruined, their people no longer who they are, and taking over their lands.

Even Fluttershy, the Element of Kindness, has rejected the way Equestria is going. By failing at all of these we’ve also falled at Loyalty because we failed to be true to ourselves.

Upon hearing this, Rainbow Dash smashed her locker so hard that it made a huge dent and she started cursing up a storm but none of the other Wonderbolts, even her captain, tried to calm her down.

+}{+

“And finally, we failed Friendship.

All of us know the lessons that Twilight Sparkle, the so-called Princess of Friendship, had learned in Ponyville.

I was there. I read her books. Attended her sermons.

And I once knew her personally growing up.

I can tell you right now that Twilight failed her own teachings. Because everything we are doing is proof that Twilight can preach all she wants, but she failed to put what she learned into practice.”

Everypony near Twilight backed away as her mane was lit aflame and she gritted her teeth with rage before teleporting away. A large explosion was soon heard nearby and from the windows one could see a towering inferno erupt into the sky.

“But this isn’t the worst of the lies. No, another lie that you have been told is that our world is fine. That Princess Celestia left behind the means to have the world’s sun and moon continue to move without us.

This is...this is a lie.

One of the worst lies of them all....”

+}{+

“Ask yourself this: who is controlling the sun and moon back home? The Princesses will tell you that it's Saddle Arabia, but this is a lie.

The sun and moon are not moving.

They are stuck and without them moving...all life back home is dead.

Every griffin, changeling, minotaur, dragon, donkey, cow, yak, diamond dog, kitsune, lycan, hippogriff, siren, wyvern, abyssinian, and other races, including ponies who didn’t live in Equestria?

They are all gone.

1.2 billion lives. Dead. Because of Equestria leaving the dimension.

That is 1.2 billion lives on Equestria’s bloody hooves.”

Around the various concentration cities where all non-pony residents had been living, a great sorrowful cry was heard across the fields and skies.

A cry of endless sorrow and grief.

+}{+

“You may say I am a liar. You may think I am joking. Or maybe you just don’t want to believe it. But this is the truth.

The truth is that Equestria is the monster in the dark.

The demons under the bed.

The bad guy that is trying to destroy this world.

I, and many others like me, have joined with humanity to stop this. I do this not because I hate Equestria, but because I love her. I love my country, but that means fighting her when she is doing something wrong.

And right now, you are in the wrong.

So I urge you all, citizens of Equestria, to remember who you are. To think for yourself. To stop and listen to what is inside your heart. Do not listen to the Princesses for they are lying to you. Listen to your own mind and soul. Rise up and reject this sick infection that has plagued our beloved home.

We will stop this war.

We will save humanity.

We will rebuild Equestria into a nation that she is supposed to be instead of a nation of insanity and bloodshed.

Join us as we fight on to tell Princess Celestia, Princess Luna, Princess Cadence, Princess Twilight, and all their allies two simple words...”

“NO MORE.”

And then the broadcast ended.

For a long time, the entire nation fell into silence as many stood or sat there in thought and many wondered what would happen not knowing that the dominos had started falling.

And there was no stopping them.

+}{+

Lyra took the big glass of water provided for her in the sound booth before exiting the room. The Doctor was waiting for her with a big smile on his face as she took a deep breath and asked, “So? Did I do well?”

The Doctor lifted his amulet and saw the orange gem glowing. He smiled and said, “You were fantastic.”

Author's Note

What the Jumbled Text Says: "The Doctor is Our Enemy And Must Be Destroyed"

As always, please help out at the NegotationsVerse TV Tropes Page. We even have a Regeneration Focus section: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 8

"That is the smell of death, Peri. Ancient must, heavy in the air. Fruit-soft flesh peeling from white bones. The unholy, unburiable smell of Armageddon. There's nothing quite so evocative as one's sense of smell, is there?"

- Sixth Doctor

"Logic, my dear Zoe, merely enables one to be wrong with authority."

- The Second Doctor

+}{+

***

Ever since she was a little griffin, Gabby had always wanted to know her destiny.

Growing up in Griffinstone, most didn't care about their futures or what they wanted to have as a dream job since, most of the time, griffins were only concerned about making day-to-day ends meet while ensuring no other creature was screwing them over.

It was no secret that griffins were going through a lot in the past one hundred years since the last downfall of their long list of ruined civilizations. Now they were scattered remnants fighting each other for resources or just leaving each other alone. It was kinda envious how the ponies of Equestria managed to keep one going for a thousand years while griffinkind had new systems of government every one hundred to three hundred years.

Gabby had been lucky. She grew up with parents who loved her and encouraged her to find happiness outside their homeland's sad state. So she decided to become a courier that traveled worldwide, giving her various experiences that shaped who she was today.

She was quite an outcast from her fellow griffins because she was always cheerful and happy, always doing her best. After all, she believed that the world would be a better place if everyone did their best.

Her parents worked hard with smiles, so why couldn't she?

It didn't leave her with many friends. The closest one she had was Gallus, and he was more of an acquaintance than anything since he had no parents and was forced to live on his own, but it was clear he wanted to be on his own most of the time.

Still, Gabby kept trying to find something to help her impact the world more. A chance to discover what she was meant to do in his world. And then fate gave her a twist she never saw coming.

While delivering a letter into Equestria, the entire nation was suddenly transported from their old world into this new one. A world with different creatures, environments, and beliefs. It amazed Gabby that this had happened, yet she was also frightened because she had left her parents behind.

And she wasn't the only one. Numerous non-ponies visiting or immigrating into Equestria were taken from their world against their will: griffins, donkeys, Non-Equestrian ponies, diamond dogs, minotaurs, cows, Abyssinians, and a parrot.

There were a lot of complaints with demands to be taken home. More than one was arrested, but the Princesses told them they couldn't return to their world.

Despite being given automatic citizenship, welfare, and even their own town built for them as compensation named Wayside, many like Gabby still felt it was unfair. Grandus knows what her parents were thinking upon hearing her gone like that. However, Gabby knew others were also feeling the same pain as her, so she resolved to help them. She soon became involved with their new community and helped them out in whatever manner possible. Gabby soon made new friends and started to adapt to her new world despite never being allowed outside of it.

There was Iron Will, who was in charge of security. A bold and loud minotaur but was quite sweet once you got to know him. He also made sure to toughen others up and had them learn self-defense. He also was good at ensuring Wayside didn't get screwed over by less kind ponies seeking to rip the town off.

Capper was an Abyssinian who knew how to get supplies from outside Wayside, and no creature knew how, but it was suspected he was a thief or con artist before being transported here. Still, he ensured to get you what you needed and only asked for favors in return. Although once or twice he would do things pro-bono.

Captain Celaeno had proven to be the town's best leader since she had managed her own crew before (Sadly, they were outside of the Equestrian Borders while she was scouting ahead on her own for a place to rest, and they were left behind). Everyone respected her wisdom and leadership, especially now that they were all on the run.

And finally, there was "Agent P." He had only shown himself to the four of them because he had no other options. Especially since his species was an enemy of the Equestrian Government. He only asked for sanctuary in exchange for spying on the government for them with his skills. Although they were reluctant at first to trust him, his information proved valuable as he began to show that the Equestrian Government was not all benevolent as it made out to be.

Princess Celestia and Luna forbid the non-pony races to interact with humanity or leave their borders for reasons that didn't seem obvious before.

Everyone in Wayside had to rely on Lyra Heartstrings' book to learn more about society, and Gabby was fascinated by them. She was amazed by what humanity could do, good or bad, and they reminded her so much of griffins it made her homesick. She longed to visit places like Latvia, Mexico, America, Kenya, and Germany. But they were denied every time she and others requested the right to travel.

The government said it was for their own protection since mankind was still adjusting to seeing aliens, but Gabby's secret friend, Agent P, told her it was hogwash. Agent P had claimed to her that Celestia was keeping them locked in her for some unknown purpose and was planning on doing something with humanity.

It turned out he was right because the war happened.

A war that Gabby never wanted.

In fact, everyone in Wayside was against it, but the Equestrian Government forbade them from speaking out loud and threatened to take away their funding if they did anything. They even started building checkpoints and fences around the town while gathering up other non-ponies who had managed to rile things up and throw them into Wayside.

It was becoming clear that Wayside was not a town but a prison.

Only Agent P had the means to escape, thanks to his particular skills. He was the only one who could give them information about what was happening outside.

When he returned one day, he was pale as a ghost and informed them of their future when this war was over. Agent P revealed what he had overheard from Princess Celestia's top scientists after weeks of being "friendly" with them.

Princess Celestia had no intention of letting anyone return to their old world, pony or otherwise. Worse still, Princess Celestia had plans to make a Conversion Potion for non-humans. The goal was simple.

A new planet for Equestria where only ponies existed.

It was clear that they had to escape. At times, Gabby might have been envious of ponies having cutie marks, but she loved being a griffin. It was what Grandus had made her, and she would die before letting that change. She had seen one or two Newfoals and knew something was wrong with them. She would not be like that.

Plans were made for an escape to the human lands when they heard about the changes of the war. The Defeat at Osaka and the death of Prince Shining Armor had made Equestria take a backpedal that changed everything.

However, it was Lyra's speech that had been the final straw.

Wayside wasn't allowed radios, but Capper had managed to get a few in for groups of creatures to hear. Once they listened to the true fate of their world, there was great sorrow and cry of pain for all involved. Gabby had spent the entire day and night sobbing into her pillow and screaming so loud her windows broke. She punched her bed mattress, threw her belongings into the wall, and got so drunk she had to puke into her toilet multiple times.

Their world was gone.

Everyone was dead because the Princesses were not controlling the sun and the moon.

Everyone in Griffinstone, and all other griffin lands, were gone. Her parents. Gilda. Gallus. Grandpa Gruff. All of them were with Grandus now, but they didn't deserve to die like that. None of their families, friends, and fellow members of their species deserved to die like that.

That was when every creature made the decision.

They had to leave.

They were all that was left of their people, their culture, their history, and more. They had to do what it took to survive for their sake to live on. And even if there was no way out, it was better to die than become prisoners to the ones that genocided their people.

Of course, they couldn't do anything half-stupid. They had to plan it out. They pretend to still be ignorant of the truth while spending months planning their escape.

The diamond dogs started digging tunnels to get them out while ensuring they collapsed to stop others from following.

Iron Will and his fellow minotaurs were using their smithing skills to make weapons and armor from any metals the diamond dogs found.

Capper and his fellow cats were stealing supplies under the nearby soldiers' noses with none the wiser.

Agent P had been vital in getting any information they needed and scouting ahead.

Meanwhile, Gabby had been their prime messenger to everyone. Since she was a courier, none of the inspecting soldiers would suspect her of carrying their plans.

Captain Celaeno had been the brains behind everything, especially when she learned there was a shipping port not far from where they were. While she might have been an airship pirate, she still knew how to operate a standard sea vessel, and training began with others on how to properly manage a ship.

The final and most important part came when Agent P contacted someone from The Underground Railroad who reached the U.N. They were more than willing to help, but the barrier was the problem. They would have to sail all the way to the South Atlantic Ocean, where members of the British Navy would meet them and escort them to the Falkland Islands. It was a risky operation, but after every creature voted unanimously to go forward with the plan, it was agreed.

And so, five days ago from today, the entire village of Wayside escaped under cover of night in the finished tunnels. They collapsed on the way out as everyone flew or ran together to the nearby port while the donkeys carried everything essential for the trip, including their young. The surprise attack had managed to give them the edge, and they took the port but had a few casualties along the way.

However, by dawn's beginning, they had started their journey.

Sadly, they underestimated the determination of the Equestrian Navy as they were now right behind them with their warships. They had fired a few warning shots, but Captain Celaeno urged them to keep sailing. There was no mercy for them if they surrendered.

It was this or nothing.

Gabby watched as the warships chased after them, but she was not afraid of dying. Her family was waiting for her in the afterlife, and if today she would meet them again, so be it.

"You scared?" Gabby turned around and saw a black feathered griffin with deep purple eyes and red tips for his wings staring out into the sea with her. The ships ordered them to stand down or be fired upon, but they ignored them. "From the rate of things, we're not going to make it."

"I'm not scared," Gabby answered with a smile. "If anything, I'm proud we did our best. And hey, where we're going after this will be nicer. We'll see each other again without pain, hunger, or fear."

"...My people never believed in an afterlife. You just died, and that's it," The black griffin sighed as he looked down. "Well, except my brother. He always...he always believed in things that are different from the rest of us. I always thought they were stupid. I would give anything to hear them again."

"You know if this is the end. Maybe you should lose the disguise? I mean, everyone knows what you are already, Pharynx."

The black griffin soon changed into the last living changeling known as Pharynx. Former Head of Border Vanguard of the Changeling Hive.

He and his group patrolled their borders when they were under attack by the Royal Guard investigating their patrols. Pharynx and his group fought bravely, but he was the only survivor who was being taken to Equestria for interrogation.

Fortunately, the teleportation into the other world confused the Royal Guards, allowing Pharynx to escape and kill them before hiding out in Equestria. He had also tried to see if other changelings were caught up in the teleportation, but he was the only one. It was a case of bad luck.

Naturally, everyone in Wayside was afraid of him at first and didn't trust him when he revealed himself, but over time he became more than just their contact and spy. He became their friend. And in turn, Pharynx found his new hive.

The day they learned what happened to their world, Gabby and her friends saw Pharynx sobbing uncontrollably and stating he wanted to die. He had lost everything he ever loved, cared for, and regretted so much, including never being a better brother to the one member of his family he truly loved: Thorax.

It was then that they knew that Changelings were no different from the rest and hugged him that night together.

"I wish I could have continued fighting...for them, you know?" Pharynx whispered as he took a deep breath. "I wish I could have lived a little longer. To see the human world."

"Me too," Gabby whispered with a smile as she hoofed his hoof and held it. Pharynx looked at her and smiled back before turning to the sea.

And then a large burst of water erupted from the sea.

Not from their side but from the direction of the Equestrian Navy.

Gabby and Pharynx were knocked off their legs, and others on all the ships started yelling in surprise. Gabby gripped the edge of the port and looked up in shock to see the boat in question beginning to sink. "W-What the?! Did we fire a cannon or something?!"

"Impossible! The ships have no weapons!" Pharynx shouted as he looked around. "We're still in the barrier, so it cannot have been the British Navy!"

Suddenly, there was a significant shift in the ship's movement, and they started to go faster. Someone shouted something about looking into the water, and the two proceeded to do so. "What in the Queen's Crown?!" Pharynx exclaimed in surprise.

Gabby was just as shocked as he was because of what was pushing them faster: Whales. Actual large blue whales were moving their ships away from the Equestrian Navy. That wasn't all, in fact. The loud sounds of whales could be heard just as far away, and Gabby gasped. Whales, as large as the ships themselves, had flung themselves out of the sea and onto the Equestrian vessels, crashing down on them. The entire fleet was being attacked by whales and sending them into disarray.

"H-How is that possible?!" Gabby asked in disbelief.

And then there was a sound.

The two looked behind them and saw something materializing. It was a large blue box with a light on it. Pharynx's jaw drop. "It...It can't be... It's him."

"Him? Wait a minute, you mean..." Gabby gasped as she recalled some of the stories and tales Pharynx shared with them over the months. About how a pony came in a blue box with companions that had turned the tide against Equestria. Giving them defeat after defeat with miracle after miracle. A name that had made Equestria tremble with fear:

The Doctor.

The door opened once the blue box stood still, and out came two individuals: A stallion looking like some kind of admiral while the other was well known: Fluttershy, the Element of Kindness, and the defector from Equestria.

Upon seeing Pharynx, Fluttershy yelped and ran back into the blue box, but her fellow pony ignored this and walked over to the edge with a telescope despite getting stared at. "Wonderful! Seems to be working nicely! I knew that the undersea creature communication device from the Sea Devils would come in handy one day. All we had to do was use your ability to communicate with animals, Fluttershy, and we'd have our own navy to handle the Equestrian armada."

Upon hearing no response, he turned around. "Hmm? Fluttershy? Are you back in the TARDIS?"

"D-D-Doctor! There is a changeling here!" Fluttershy cried out as she pointed from inside the TARDIS.

Turning to a shocked Pharynx, his eyes widened before smiling. "So it would seem! It seems the changeling race survives after all! Always did like your race. Had a companion who was a changeling. Khameleon, her name was. Although she's actually a Star Changeling, one of your cousins on planet Charade. You look familiar, though. What's your name?"

"Pharynx..." He answered.

"Commander Pharynx!" The Doctor said as he took the Changeling's hoof and shook it. "Great to see you again. Didn't recognize you without your color change. Although I think this would be the first time for you. Timeline change and all. Otherwise, our first meeting would be at your daughter's wedding to Dragon Lord Ember's son. Good thing we stopped The Rani that day."

"...Huh?!" Pharynx asked in disbelief.

"Oh, right. Sorry, kinda getting ahead of myself," The Doctor said as he smiled at them. "Well, who is in charge around here?"

"Um, Captain Celaeno," Gabby answered, pointing down the ship.

"Wonderful! I'll go meet with her. Fluttershy, please watch things from here?" The Doctor asked as he headed out.

"Okay..." Fluttershy whimpered.

Gabby blinked a few times before turning to a confused Pharynx. "Your daughter married a dragon?"

"I don't even have a daughter!"

+}{+

Princess Celestia had been at war before against multiple different nations throughout her long reign. She had soaked her hooves in blood, led legions against harsh conditions, and performed great strategies that are still respected today. Some wars were more brutal than others, but right now, the fight against humanity is becoming the most challenging and frustrating war in the history of Equestria.

Ever since the Defeat at Osaka, the entire war effort had turned against their favor. With a cure to the Conversion Potion now rapidly made, one of their biggest weapons was rendered moot, which affected their battle strategy.

Using the Conversion Potion was a means to cause confusion among the military and civilian population, which would allow their armies to strike while they were scrambling. Now that there was a cure, it was a waste to use it as the humans would use the treatment on themselves, and they were mass produced in every area of the world to the point that many had at least five or more cures on them at all times.

With reluctance, Princess Celestia had to put all manufacturing of the potion on hold. The good news was that the income used to make it could be given to alternate war ideas proposed by Twilight and other scientists.

Since force was the only thing left, significant war spending was sent towards creating better armor and weapons for their forces.

The two biggest weapons were the Orichalcum Armor and Crystal Shooter. The first was a breakthrough founded by one of her top scientists, Professor Helix, who had been trying to get more funding for his personal projects. Once he had it, a few months later, he had managed to create a means to craft the dense metal of Orichalcum into becoming a means to use for armor. The famous metal had always been so thick and hard to move even with magic due to its chemical structure, so rarely was it used save for fortifications and building construction. But with his new solvent that weakened the weight of the metal, it could be appropriately forged into armor. It was tougher than the Royal army's standard armor and could take bullets much better. It had already helped lower casualties by 18% on the battlefield.

The Crystal Shooter was Twilight's invention. A means to match humanity's prime weapon of firearms.

Personally, Princess Celestia hated using weapons inspired by humanity, but with the war going as it was, she had to resort to measures she disapproved of. It didn't help that Twilight went through with the idea without consulting her, but considering the results, it was something to merely ignore.

The Crystal Shooter was designed to be on the wrists of ponies using a specialized gauntlet with a powered crystal as the energy source. Through minor spells and mechanical engineering, it would fire a powerful laser blast that could be adjusted for damage ranging from stunning to full-on melting skin and bone.

The crystals needed to be replaced every so often once they were drained of energy, so all soldiers needed to have enough. Because of this, the Crystal Empire was forced to increase its mining operations threefold. This caused some complaints, but they were soon silenced with an agreed lowering of taxes as compensation.

Still, the new weapons of war hadn't caused a reversal of fortune.

Multiple invasions and operations had failed or ended up stalemates with humanity which was now refilled with determination.

The Battle of Chicago, the Invasion of Hong Kong, the Assault on Ontario, and the Conflict at the Suez Canal had been failures with high casualties.

Only battles where Celestia or her sister took part had success, such as the Devastation of Singapore and the Battle of Algiers. Princess Cadence was still too much in mourning to be an active fighter again, and Twilight had shut herself from the world to focus on making more powerful means of war. Neither her family, friends, or even fellow princesses had any luck talking to her except for a few minutes except to say she was "busy."

If that wasn't bad enough, Shining Armor's death had made it impossible to find a replacement.

While there were good Generals, none of them had his talent in war.

Morale was dipping, and many believed that instead of attacking, they needed to be on the pure defense and let the barrier do the work as it continued to move around humanity's land.

Princess Celestia would have agreed if not for The Doctor. He and his "companions" were always there to stop them. Appearing and disappearing from one place to another with the usual gang that had now been identified: Lyra Heartstrings, Fluttershy, Discord, Derpy Hooves, Dinky Hooves, Carrot Top, and Flash Sentry.

If it wasn't just helping out at war, it was also helping citizens escape Equestria.

Lyra's speech had done enough damage to the point that protests and riots happened in various locations demanding answers or an end to the war. Some were even demanding to head back to their home planet.

They had to be put down, but the worst was the city of Baltimare.

It had outright voted to secede from Equestria and declared itself an independent city that no longer recognized Equestrian rule. Princess Celestia personally led an army to take it back and had the entire government of the city, plus any succession activists, executed with martial law still in place.

There was still some shadow resistance every so often, but there were more important things to worry about.

Fortunately, after nearly a year in isolation, Twilight sent a message to everypony saying she had a solution to end the war and to come to the Crystal Empire at once. Not just the Princesses but also her friends.

However, it was not the Crystal Empire that they were told to appear at, but one of its top secret bases known as Fort Obsidian. It had been once King Sombra's secret base for military testing, and, despite the dark history, it was still valuable for the Crystal Empire, so it was allowed to stand, especially as the war against humanity pressed on.

That didn't mean it wasn't creepy. The entire fortress was made of grim black and green crystal architecture that made one feel like they were in a tomb rather than a fort. Twilight had been leading them through the halls, where soldiers and scientists saluted them as they progressed deeper and deeper into the fortress. Twilight had been mostly silent for the most part despite the attempts of others to get her to open up.

"So, how's the new metal wing working out for you, Twilight?" Spike asked to get his step-sister to say something.

"It's functional," Twilight said with a stoic expression.

"Come on, something like that has to be able to make you faster. I mean, not as fast as me, but still," Rainbow Dash said as she landed next to Twilight in the air. "What do you say we go through some flying exercises after this?"

"I've already been training myself, Dash. But I'm more suited for being here where I can end the war," Twilight said with a sigh. "If all goes to plan, chances are we'll end the war soon."

"Do you have a solution?" Princess Cadence asked in surprise.

"Yes. I've managed to create something that can end the war faster than waiting for the barrier to do the job for us and risk more pony lives," Twilight firmly stated.

"Oh, is it a super secret weapon?" Applejack asked.

"It's not so much a secret as it is a modification of one we've had in storage," Twilight said before they stopped at the giant double door. Using her magic, Twilight unblocked the powerful barrier spells put on it before it was opened.

Everyone but Twilight gasped upon seeing just how big the room was. It was twice the size of the throne room, and with good reason: a giant cannon was in the middle of the room while being attended to by scientists and engineers who were going back and forth on multiple levels to work.

It was practically the same height as the Royal Palace and was made from pure gold and silver. Its cogs, wheels, and circuits were beyond counting, encased in a large cylinder-like casing pointing upwards with the top part opening up a giant glass holding a sphere of what appeared to be pure magical energy.

Six smaller cylinders were attached to the glass, opened up and empty, but it was clear something was to be designed to put in it. The bottom of the barrel had the control systems, designed in a large computer-like manner, with various tactical information displayed and tested by unicorn scientists.

Mainly, it showed a map of the entire earth.

There were two big generators shaped like fat hourglasses spinning around while connecting glowing purple wires to the sides of the cannon that also had a giant floating circle shaped like a targeting system with smaller crystals circling around it. It was unlike anything any of them had ever seen before.

"What...what is this?" Princess Luna asked in shock. "I've never seen such a weapon in all my life."

"This is the Harmony Cannon," Twilight started as she walked forward and presented it. "It's been my main project for the past year, and it's finally ready."

Cadence then tilted her head. "Wait a minute...this looks..."

"It's somewhat based on the Crystal Cannon that King Sombra created, yes," Twilight answered, much to the shock of the others. "I've taken some basic parts and used them to create something new. I've done something even more powerful based on calculations combining harmonic energy, magical, and human knowledge on plasma."

"Twilight, are you insane?!" Princess Luna shouted in horror. "The Crystal Cannon is a weapon of pure mass destruction! King Sombra designed it to destroy Canterlot before his defeat! It's capable of wiping out an entire city!"

"Yes, but I've done better," Twilight said before turning to it. "I believe with this I can destroy entire countries."

There was a dark silence in the air as everypony stared at Twilight. It felt wrong to hear their once cheerful friend say such a thing with such calmness. "T-Twilight, you're kidding, right?" Pinkie nervously said while giving a twitching smile. "Y-You cannot be serious. Destroying an entire country?"

"Or two. Maybe more," Twilight said with firmness. "I haven't tested it yet, but all our simulations have concluded this."

"How are you able to do this?" Spike asked with wide eyes.

"The cannon is mainly powered by the energy of the barrier that we've managed to siphon off of for the past few months," Twilight explained. "It's the only substance of the six Elements of Harmony's magic we have available. I then took the power of several crystals and combined it with a means to create plasma to develop this new energy from its combination. I haven't figured out a name for it yet. However, I need more power to make it reach its full potential. I need all the Elements of Harmony to make it work. Not just my own. Their energy combined with the building energy of the shield should be enough to make it far more powerful than any weapon the humans have."

"Why would you even create something like this?" Flurry Heart asked in horror. "I thought we were trying to save humanity? Not wipe them out."

"Once we use this once or a few times, humanity will give up due to the sheer loss of life or the fact that they have no defense against us," Twilight stated with a slight smirk. "Not even The Doctor will be able to stop us."

"I...I think you might be going too far with this one, Twi," Rainbow Dash gulped as she pointed to it. "I mean, you based that thing off of Sombra's design. He's a bad guy, Twilight."

"This is war, Rainbow Dash," Twilight growled, which made the other rear back. "We aren't just up against humanity. We're against an alien whose species mastered time travel and space travel before our race was even born. We're against a being who made monsters afraid of it. If what Discord has said is true about The Doctor, then we must throw away some of our morals to defeat him, or else Equestria will lose this war!"

"...So you want to use...our Elements to power up this super weapon?" Rarity asked nervously. "Darling, are you...I mean...are you sure about this?"

Twilight sighed as she lowered her head. "Girls, I want this war to end. I've lost my brother. I've lost so many ponies under my command. Equestria herself is at risk because I predict that humanity will eventually destroy the barrier, and we'll be exposed to attack. The Doctor was able to figure out how to create a cure for the Conversion Potion so easily. It won't take long before he can figure out how to remove the barrier. Once he does, every nation in the world will attack us from all directions. They'll hold nothing back. That includes nuclear weapons."

Princess Celestia sighed upon hearing this and nodded. "Twilight is right. The barrier is the only reason we've never had to be on the defense. If we were to lose it..."

"But I thought we were supposed to be saving humanity! Not wiping it out!" Spike shouted with frustration. "I thought the point of this war was to save them by making them become something better! How can we do that by killing them in such mass quantities?!"

"We're already doing that," Twilight pointed out, rolling her eyes. "What's the difference between a battle and using the cannon? This way, we can end the war quicker and focus on recovering what we lost and helping the humans faster after they surrender to us."

"But to use such a means to do so? Using a weapon of mass destruction?! One based on a tyrant?!" Spike yelled with disgust. "This is not only dishonorable. It goes against everything we believe in as Equestrians."

Princess Luna turned to her sister. "Sister, what do you think?"

“I...”

Ǘ̵͕͍̤̹̪̘̺̰̥̪̆̒̓͗̈́͜͝ş̷̆̄̑̊̈́̓͒̿̏͛̆͆̄̏ĕ̸̡̨̛͇̞̟͖́͂͊̒͑̽̇̈́͗̑̕ ̶̡̙̲̫̙͉̪̠̟͙̪̦̗͔͙̑̐͌̽̓̋̊i̸͔̽͊͂͊̏̍͛̈́̉͒̀̚͝t̴̡͈͉͔̳͖̟̹̥͕͈͍̥̮͋̿̅̌̿̂̑͐́̚.̶̧̜̖̪̤̮̗̭̯͎̙͈̭́̐͑ ̸̺̥̘̦̙̩̫̉͜Í̶͙͚̖͚̻͎͈͇̇̋̋͗͗ ̵̨̡̨̢̦̹̗̞̠͉̤̝̹̦͕̓͘̕c̸̜͎̞̲̺̩̮̄̆̉͐͘ͅo̷̡̨̨̗͚̞̭͇͚̜̖͓̙̓m̶̨̪̯̟͉̲̗͉͉͔̯͇͍̮̌̽̇̈̀͊̕̚m̷̢̙͕̝̹̰͙̰̪͇̻̅ǎ̸̛͙͈̝͚̮̤̼̊͑̃̓̑̽͐̀͠ņ̴͍̠̹͙̻̻͕̱͉̓̀̉̊d̵̡̲͍̦̹͚͈̬̻͑̽͒̂̋͛ͅ ̵̧̢̨̘͕̙̠̩̹͓͇̘͋͐̏̒̃̌͋̓̚y̸̡̛̱͉̦̯̼͗͂̒́͂̈́̊͆̚o̶̖̥̖̯̤̻͔̺̝̥͔̗̗͒̋͆̾̈́̒͂̾̔̿̈͠͝͠ũ̸͔̀̎̇.̷̧̞̹̣̰̣̺̰̳̃̓̓́̄͑̕͝ͅ ̷̨̭͉̼̬̘̐̓͊̔̾̕̕͘Y̶̡̥̘̹͈̻̭̻̦̘̝̩̹̯̋͆ȯ̵̧̡̠̙͉̱̤͓͙̘̊u̶̧͇̝͓͚̠̺̭̼̩̤̝̰̝̇̎͐̂̈́ͅ ̵͖̆̐͛̓̋͘̕̚w̶̫͇̹͎̄̓̀̊̑̿̚͝į̵̘͖̭̹̻̹͚͑͛̈́́́̈́͘͝ͅl̶̗̥̼̣͇̯̩̯͍̭͚͆̐̉̿͆̑̌̐̑̂̚̕͝l̶͚͓̱̬̀̓͗̈́̈́̒͒̌̏̈́̕̕ ̶̯̝̉̈́̍͊d̶̛̪̳̭̖̳̳̉ȅ̶̡̥̳̟̿̉̑̓̈́͛s̷͙͓̠̟̉͛̉͋͑̒̃͘t̴͈͚̥͈͙͎̺͗̇r̸̺̫͎͍͗̂̐̎̈́͛͝͝o̶̢̡̧̭̣͉͉͕̖̙̊̎̅̊̍y̶̧̢̼͍̝͓̿̐̚͠ͅ ̶̛̛̣̗̬̒͌̈́̉͂͗a̴̡͈͖̠̣͙̭̜͍̗͙̓̓̅̒̈̄͝ͅl̷̨̧̘͚̘͓͓̑̈́̇̎̀̔͋̀̉̕͝l̷̯͎̟̼͗̄̈́̇̀́̓̿̄̆͘͘̕ ̷̨̘͕̜̪͙͕̞̂͜y̴͕̖͖̽͂́̑̾̋̕͘͠ó̷̢̠̹̳̲̹̥̪͍̦́͘ư̵̪̏̔̌̅̒͠ ̵͔̬̯̙̹̗͔̫̘̼̰̔̃c̷̺̞͈̫͈͉͖͍͔̘̐̂̒̄̌̈́̈́͗͘͘͝a̶̡̗̲̬͈͎̔̉̑̂̋̊͆͂̈̆̅̅̔͑́ņ̸̲̘̭̹̆ͅ ̴̧̛̘͉̗̺͔̘͗̍̔̈́ͅȃ̶̻̯͖͖͕͇͇̼̀̃n̵̛͎̘̞͙͑̏̈͋́̎̕̚̚͝͝ḏ̷̡̛̖̮̹̭̮͗̓͒̈́̒͂̂̽̇͘͜͝ ̴̡͔͎̜̱̪͑̒͐c̸̱͑͌̚ȃ̷̬̲̻̬̟̻̪͔̣̯̜́̄̂u̶̳̤̬̣̖̖̙͓̔͗͋̎̔̓̾̑́̈͑̔̊͝͝ͅş̶̝͚̤̻͖̯͙̳̮̜̻͂̅͑ȩ̶̢͇͚̱̟̬̟̺͍̋̃̑́̔̑̏͌̄̀̏͝͝͝ͅ ̵̢͎̬̣̟̘̫͙̦͕̊̉͌̌͋͛͂̒̚͝͝c̶̛͖͇̉͂͆̏͋̕ḩ̷͍̩̖͓͍͈̞̩̹̱͇̰̈̀̕͘͠a̶͈̜̋ȍ̶̩͍̖͚̙̝͇̻̈̏́͊̀s̶̢̛̭̩͍̆͒̈́̀́̄͌̇̉͐́͌ͅ ̶̳̘̍̏̑̒̓̄͛̓̓̅͌͐͝ȉ̸̢̨̹̣̱̬͈̞̭̪͍̟͌̿͌͒͑̇́̈́͜ṉ̵̨̗͖͎̞͙̮̉̑̓͂̌͊̇̀͐͐̇̀̊͗͜͠ ̴̙̥̫̠͈̓͆̀̊̉̍͠m̵̨̡̡̧͈̠͓͖̲̮͎̙̼̟̎̊̒̽͂̆̕͝ͅy̵̡̢̼̜̰̫̠̝̖̮͇͖͉͎̭̍͋̔ ̷̨̧̡̛͚̪̝̩̯̳̳̖̞̂̾̈́̈̒̈͒̽̀͗͐͝͝ͅñ̷̟͌͌͗̚a̷̺̭̲̰̅͠ṃ̷̧͇̥͍̰̭̘̥̲̼̖̆́͒̐̿̅̚̚ͅͅe̶̤̹̪̣̤͙̜͓̮͔͎̳̍̓̽̅͛͜͝ͅ.̷̨̫̤̣͓͎̱̭̪̱̲̯̆͗̈́̍̕͘͝

“Ugh,” Celestia winced as she rubbed her head.

“Sister, is something wrong?”

“I...I...”

Ȳ̴̨̼̱͍͂ọ̶̧̡̡̫̖͇̗̰͖̭̗̰͚̔̌̈́̿͋̄̉̚͘͜u̷̧̩̤̽̆̇̇̔̀̇́͘ ̷̯̝̣͉̼̟̮͍͎̞̟̔̔͋́͌̕͝ͅh̶̛̦͌̒̎̄̅́͗͘̚̕a̶͚͎͕͍̦̎̈̈́̀͋̽͆͗̎̾̀̀̾̄̿ͅt̵̗̬̼̯̳̱͗̆͜ě̴̤̻̭̬̯̟̫͚̈́͒̾̿̑͂́̉͋͒͋ ̷̫̺̮̩̬͍͇̚t̴̛̺̎̀́̂͐̿̂̕h̵̝̋͜e̶̠̱͖̳͙̗̠̰̤̗͕̹͆͒̈́̈́̈́́̒͆̋͐̍̾̕͜m̷͖̪͈͇̺̀̋̍͋̑̄̎̽͑̎̂͝͝.̶̧̻̰͌̄̔͝ ̶̡̧̤̞̞̜̰͚͓͉̞̺̇͆̾́̓̋̃̅͆̏͑̈́T̸̜̖͖̜̩̱͎͔̯̖͐̈́̈̑̀̐̆͛͆́͊̀̚h̶̛̙͓͕̦̹̤̙͙͙͓̳͇͍́͌͂͒͑͆̍͐̀̐͒̎͝ė̸̢̹̪̖̼̘͓͚̝̝̃̅̓̆̇̽̇̑͑͛͆̚̚̕y̵̢̯͋͛̓̈̀͌̍̍̃̀̈́̂͝ ̸̭̠̫͔͖̇̏̂̄͂͘͝k̴̛͍͋̽̐͊̀̄͑̔̾̕͝ͅͅị̶̡̧̤͍̘̲̯̼̼̻͓̔l̵̨͍̹̙̥͉̪̯̬̞̝̭͕̉̈̇̃͌̈́͌̈͜ͅl̶̼̩͙̳̞͇̖̦̓͋̾̐͊̀͜ē̵͎͕̳͈̰͠d̴̨̛̓͒͂̅̑̓̂̏̌̽̂͝ ̶͖̔́̒͛͝y̸̡̛̺̹̤̭̾͛̌̉̅̅͋̉́͗̚̕͜ǫ̶̡̛͕̘̟̳̗̱͔̙͕̠̋̓͋̆̀̒͑̔̚ų̸̫͇̥͎̞͇̫̩͎̝̯͈͇̄̆͂̉̊̒̓̚͜͠r̷̞͚͕̳̪̲͉̻̭̍̑͜͝ ̶̥͈͔͛́̆̈́̊͋͐͌̓͐̐͆̑͜͝d̶̦͈̺͝a̸̮̝̯̠͎̣̯̿̾͂̐́̏́̔̈́̓̀͘͜͠ù̴̢̜̜̩̖͙̮̱͓̐͂́͠g̸̦͉̰͎̝͓͈̜̭̝̩͈̬̺͗͑̋͋h̴̡̪͍̤̉̂͛̐̏̀͝ť̶̥̊͌̎̊̇̎͒̄̀̉ḛ̷̢̜͉̥͇̳̦̹̾̍͐r̷̫̭̔̐̔̈́̐̑̿̄̿̏̊́͐͝.̶̱̺̓͊͛́̆̅́͐ ̶̲̞͔̩̹̑̀͘T̶̬̱͍̜̰̘̙̘͚͉͋̃́̄̈́̑̒̈́ͅh̸̢͈̱̩̖̣̘̻̦̑́͂̈́́̋̔̉̇͐͗̍͗̽͠ë̷̢̫̫͜y̶̧̡̙̭̭̪͈̫̟͈̰̯̩͕͇͌̈̈́̅̏̍̿́̄̉́̃̌͘͠ ̸̯̱̪̰̘̜̠͙̪̲̫̮̣̗͉̇̍͒̀̋̅̇̇̽́͊͝͝͠͠ẇ̴̰͚̠̟͆̿̔̽͋ḭ̷̢̛̛̠̦̫̰͉̲̺̞̜̖̺͖̏̀̍͗̃̀̃̒͜͝l̶̡̤͔̝̹͈̘̼̹̗̹͇̟̓͋̅̓̉̚͘͘͝͝l̸̰̥̝̝̭̠̓́͊̄͆́̽͌̐̐̔̍̊̐̕ ̴̪͕̞͎͂̈́̾̒͒̚̚͝k̶̡͚̯̩̘͈̳̙͔̯̣̈̂̐̽́̽͆͘į̵͍̗̱̩̣̗̫̞̹̠̙͕̭̀̎̄͗̋̑͜l̷̝͆̓̓̔̆͛̑̒̈́̊̄̀̚͝ļ̷̨̡͔̦̲͓̬͈̻̖͉̗̂͊͊͜ ̵̛̤̼̚y̵̨̭͖̰̺͍̟͕͉̜̤̖͛͊̐̌͜o̴̡̧̤̝͍̣̙̪͓̮͖̘̞̯̠͌́͂͝ú̷̠̼̱̠͚̗͉r̶̡̭̊̌̒̌̎̍̾̃̾͛̇̈̈́͠͝ ̴̰̮̰̤̻̞͇̤̋́͒̽̀́̓f̴̡̨͔̯͙̞͈̹̗͓͉̦̜͛̆͗̍͂͛̃̒̊̒͒̏̍a̵͖̩̝͑̋́̀͊̕͝͠͝m̷̥̞̗̪͇̣̫̖̀́͋̀͛̒̍́̈̋̏͑͐̐ͅḯ̵̻͇͎̙͕̙l̴͕̣̲̳͕͑̿͂͒̀̈́̚͘͝y̶̢͈͕̟̲̻͉̲̳͍̪̟̭̆̔̊̃̕͝.̷̨̫̹͎̼̬̹̯̈́̈́̌̆̾̑̓́͒͐̆͌͋̊̏͜ ̵̳͚̯̠̈̈̀̍̎̑̑Y̴̢̭͕̤͕̘̪̠̟̜̫̪̪̻̔̈́͐̋́̽̊͐̇́̍̕͠ͅọ̴̧̱̲̳̫̤̭̠͔̜̺̘͉̎̈́̔ͅư̸̡̆̋́̌͂̔͌̈́͝ ̵̛͚̤̥̦̘̈́̉̾͋̎͊̀͑̄̊ͅm̵̨͔͔̙̜̬̲̖̙̣͉͋̓̍̓ũ̸̗͈̱̤̣͆͂̽͋ș̵̗̼̝̩̼̱̈͆̈́̍̋͛̂̍́̓́̚͜͜͠t̵̢͖͇̪̙͋͛̄͛ ̸̝̳͈̦̣̦͎̙̯͇̼̼̩̅̆͌̒͠d̵̡̛̼̖͎̳͓̒̈́̿̔͐̽̀̈́͑̆̎̿̚ẽ̷͖̲̞̝̳̬̮̬ͅͅs̸̺̘͔̘̋̾́̈́̈́͑̓̃̉͊͐͆͘̕͝t̷͈͍̼͇͕̦͍͉͍̻͉̼͚̒̄̎͛̉̾͝͝ͅŕ̵͕̑͊̐̐̓͆̔͒̚̚͝͝͝ô̷̬̥̖͔̝̻̩̲͙̪̺̔̈́̑͗̇y̶͓̥̬̭̑̃̋̒̋̒̈̎̀̀̓͝ ̷̗̤̦̪̘͔̣̼̟̼̋ͅṯ̴͊̎̚͘ĥ̶̯͉̹̖̥͇͇̺̏͌͂̆̔̅͗̑̍̕̕e̴̦͕̳̩̒̉̉̓̏̆͌͜͝m̵̘̙̪̤̑ ̸̳̯̊͒̎̏̽̉́̍̇͒̊̄͘̕b̷̤̹͔̗͐͊́͛̉̇͗͊̏́̐̐̄̚͝ḙ̶̡̡̭̼͈̻̤͐͊̎͊͋̈̿̓̚͠f̸̧̡̛͈̞̤̺͈̗̹̪̞̲̘̦̿̓̐͜o̴̘̱͎̟̤̤͓̲̠͖̙͔̰̺͙̿̇̃̏͌̊̊̀͐̈͝͝r̸̫̳̽̋̂͊̽́͆̀͋̄͝͝ȩ̸̪̣͈͉͎̝̪̜̦̩͍̗̏̀̑̐͒̄̓̾̈́̎ͅ ̵̧̖̬̖̖̙͈̱͈̝̹̥͈̿͆̉̑̏͒̋ͅṯ̷͑̐͛̑̏̔̽́͆̋̀͘h̴̛̩͎͎̙͙̳̯̤̽̒̅͑̐̌̋̿͜e̷̡̡͙̺̋̌̃͆͘̚y̶̡̛̥͙̳̞̳̼̘̟͌̌ ̴̳͚̤͆̓͠ḑ̵̢̹͍͓͌̆̅̍̏̿̆͜ẽ̷̡̨̨̝̰̝͇̬̺͕̝͖̭̜̓͐̌͋̍̾͐̒ͅŝ̸̨̢̛̖͔̤̻̯͙t̴̨͖͖̝̲̗̣̱͙̦̞̠̊̆̋̒̉͛̀̉͋̈́͗͐͠ͅr̶̛͇͒͆̐̿̏̕̕ò̶͕̦͈͖̣̯͔̱̹ͅy̶̧̛̛͂͌̅̀̓͐̐́̊͛̈́̚͝ͅ ̷̱͇͙̱͎̭̟̾̀̄̽͂̄͊͊̋̀͋͑͊y̴͈̻̗̻̯͌ơ̵̢͙̥͉̝̱̜͔̼͔̖̘͌͆̊͌̀̆́͊̑͗̇͝͝͝ų̶̳̦̜̥̯̽͋̽͊͝͝.̴̧̨̯̟͎̞̣̩̃̑̀̚͝ ̴̡͙̺̳̞̺͇̥͚̘͙̌̆̋̊̉̌̾͐̐̈͗̏͠͠Ÿ̵̡̛̩̺͉̹́̍̂̈́̈́͊͗͘͝͠ơ̵̟̻̹̳̈́͋̒͆̂͋͊̉̀͛̚͝͝͝û̶̧̢̢̼͎̙̙̣̰͓͉̯̣̖̯̂̉͆́̀̆͒̏̑̀̾̌̾̕ ̸̧̖̮̘̦̝̓̐̇͐̊̅̈́͋͛̈̌̎̕͜͝ͅw̸͇̬͇̺̳̩͉̋i̴̧̡͉͍̰̤͚͙̟̜̘̪͑͆͋͂̾̇͑̈̌̎͘̕͠l̵̥̙̩͖͓͐̇̀͛̐l̶̡̳̰̰̥̞͇̮̜͙̩̲̂͌̎̅̋̉̀̂̄́̉̎ ̶̧̘̭̝̩̳͔̜͉̙͎̒͑͋͗̓́d̶̢̛̛̘̯͂̇̈́̂͋͛̏̚̕͠ė̵̢͚̥̳͓̖̝̩́s̵̳̤͈̣̈́͗̏̑͋̏̐͘͝t̴̮͉̉̓̾̅̓̃̌̒͠͝r̸̢͈̙̼͇͍̟̦̂̿̈̈̔̚ö̷̡̤̱̣̠̼͍̆̓y̷̪̦̞̠̼̺͊͝ ̴̠̦̬̺͆T̵̞̰̭̥̦̖͙͕̲͉̙̅̒̋͗͝ͅͅh̸̢̧̥̭̪͕̮̙̺͉̋̑̏̉̅̾͊͛͋͌̊̀̚̕͘ͅḛ̵̡̡͖̘͕̪̠͓̙͍̝̑̌̆̏̍͋̍ͅ ̶̢̡̬̜̲̟̪̯̺̰͇͈̦̈́͗͋̏̊͑͋̃̒̿͜͝D̵̢̤̳̘̮̼̬̞̪̠̝̘͕̆̅͒͋͛̔̋̂̿̈́̉͊͜͝o̴̡̹̜͎͖͈̼̯͕̫̤͛̿̔̓̒͝͝͠c̶̢̝̠̣̪̻͕͉̰͇̑̾̀̈́͠͝t̴̜͇̙̮̮͖͊ȏ̵̧̡͙̤͔͕́̈́̓̅͒̿r̷̦̞̖͚̟̪̣̠̒̀̇̅̀͜.̴̛͖͉̦̩͕̊̽̄͛̈́̆͌̆̽͌̕͠͠ ̷̧̼̯̭̜̬̥͕̳̟̙̦͋͜

Ugh, my head, Celestia thought as she nearly stumbled. The others were asking if she was okay, but Celestia couldn’t hear them.

Ĭ̸̢̦̼̩̦̣͍̤̪̳͙̱̺͚͑̃͑̀͘͜͠ ̸̰͆̄̾̒̒͛́̓͘͝a̸̢̢͍̼̞͎̜̹̫̘̽̃̔̍͂̏̄̍̑͗̏͘͝͠m̷̯̯̼̻̉͛̅̀ ̸͈͋̕ş̷̟̪̗̜̤̹̮̪̬̗̫̟̬͗̑͋͗͘ǫ̷̛̠̺̤̈̍͆̈́́̿̕͝͝͠ ̶̩̫͔̺̫̻̥̱̮̏̀́̑͊̊̿̋̅́̈́́ͅc̷̣͈̻͈̣̬̥̼̈́̀͗͋̌̾̿̚̕̕͝ļ̷͕̘̠̲̺͉̞̾̿̄̌͛̍͒̒͋̓̿̀̉̚ö̵͍͙̱͍͖͉̺̫͔͙͚̼́͗̀͐͗̀̕͜͜s̷̥̖̓͑̆͒͐̀͐̓͒͒̕̕̕͝ȩ̷̛̺̥̫̪̘̟̗̜̓̀̒́͌̇̑̈́͘͝ͅ.̴̯͎̭͚̐̿̂ͅ ̷̧̰̈́̌͆̊̿͌͆̅͐̋Ç̷͚̥̠̪͍̙̹̗̟͙͍͔̀͆͋̀͠͝l̵̢͚̩̙̙̺͈̒̌̏̈́́̚͝o̵͚̣͐̆̌̽͂́̽̆͐̄͆̃̕͘ͅs̸̢̨̛̙̻̙̩̻̯̠̰̤è̵̖̍̒́̌́͐̈́̓̃͝ ̶̥͖̺͙͈̹̮̻͈̭̓̔̒̿̀̐͊̕̕ṯ̸̛̛͔͑́̀́͊̈͑̈̐͂̕͘̕o̴͎͚̱̓̊̅̕͘ ̴̰̟̰̮͇̺͓͕̥̄a̸̛̼͐͋͑̿͊̑̄̄c̴̨̛̺̘̩̝̠̹̦̹̝͎̝̠͔͍͌̀́h̵͙̰̤͚͉̤̐̏̐̒͌͌͆̔͑̎̊̕͝i̶̮̱̭̘̲̻̗̤̭̲̒̐͊̐̏̀͂̋̾̿̕͜e̷̢̧̢̻̺̻̭̣̹͉̣̬͑͌̃͛͝v̸͈͈̤͔̰͎͎̲̘̆̒̅͑̈́͐̋̑i̴̡͖̹̰̇͝n̸͚̱̮͙̜̰̯̻̠̬̣͉̦̰̓̀͗́͐͘ḡ̸̨̡̢̟͍͍͍̲̫̘̹͂̋̉́̾͑̔̋̄͑̂̓̑͝ ̴̧̢̨̞̩̲̘͉̱̒̑̓̌̌̕͠ṁ̷̛̝̜̮͈̟̯͚̘̞̏̈́̊͋̏̽͌͆̓͊̀̚͝y̶̝͓͙̖͇͔̣̥͍͉͇̼̥͛̓̐́͌̋̈́͐́͌́̎́͘ ̵̨̤̘͕̩̯̣̼̯̞̭̈̆͝g̶̫̜̦̾̾͂̃͂̈́̍̍́͋̃͘ơ̶̥̝̜̲̈̅̂̇̉̿̀̚̚ͅȧ̵̺̩͙̹̬͉̣̎̃̏̎̽̈͒̕͘͜l̶̡̤͍̺̳̫̠̰̘̤̫̞̙̭̄̆̄̀͐̐́̅̊̚͝͝s̴̛̭̫̣̼͓͉̦̙̱̲̻̲͗̇̓̇̏͛̌͠.̸̧͖̱̥͍̜̃͌̍̈̏̓̋̎̐͝͝ ̶̢̜̞̬̜̭̤̱̺̭̭̻͓̄̊̽͊͐́͌̒̋͐̿̽̓̀̋ͅͅT̷̢̛̳̱͓͕̱̫̪̯͍̦̀͋̃͂͋͌̍̔͂̎̉̓͋ͅh̴̡̬̠̮̲̮͈̩̰̮̺͖̯̱̮͂̉̑͆̈́͊͐̾͆̍̋͋̋͠ȩ̴̣̪̪̘̻͍̪̭̮̜̬͈̺̻̾̎̾͐ ̷͍̳̩͉̬͇̣͂̾̈́͠D̴̮͍̝̬̲̩̱̥͗̑̓ͅo̷̢͔͉̅̇͌̉́̈̈́͆̒̾̚͝c̷̯͚̗̈̽̕̕t̴̘̥̥͐̌͗̅̈́̆̇ơ̵̡̱̬̞̮̪̝̱̼͙̹̳͂͒̓̒̊͛̈́̎̑̈́͒͘͝ŗ̵̨̢͉̮̹͓̘̤̪̹̬͇͓̫̾͊̓͊̈̎̈̊̇̈́͝ ̵̛͕͑̋̿̓̔̊̕m̶̛̺͉͈̖͍͕̮̤̦͓̻̓̎͋u̷̝͎̘̫̺̱͒͌̈̓͒̿͗̋̃̇̀s̴̨̢͓̤̞͇͓̈́̄́̈́͛̉͂͆̕t̸̢̡̢̢̛̙̗̰̝̼̗̲̯̜̏͒̋͗͂́̈́͛̈́̈͘̚ ̵̻̤͖̲̜͈͇͍̫͈͈̰̞̈́̾ǹ̷̨͙̟̺̪̜̮̯o̴̢̼̲̻͗̅̊͜͜t̵͔̺͈̝̓͛̈́ ̴͕̻̮̹̱̘̉͒̒͑̈́͌̌́̈s̸̨̘̜̦͙̗̩̜̳͕̣̜͉͊̅͜͜t̷̨̗̲͖̜̫͎͇̍̓͐̈͌̕ơ̷̘͕̖̓̊͆̅̕p̶̨̖̗̭̟̟͇̉̓̅̊͒͝ ̷̢̢̻̼͚̬̜̤̘̭̣̺̺͑́̆̾̇͜͠m̷͙͂̏͂͠͝͝e̵̡̡̧̮͕̘͚̣̪͉̓́̃͒͗̎̌̎͘̚͠.̸̛͙͕̰̘̖͖̠̲͍͚̬̖̠̲̊̾̎̎̈́͌̃͆͗͋͌́̿͜ ̴̛͓̬̱͎̮̥̔̿ͅY̴͔̞̤̜̺͛̈̆ò̴̰͒̅̈́͛̀͑̍̀̉̎̀͌̕u̸̩͖̟̐̂̔ ̶̺̩̙̼͉̗̯͔͍͎̤̦̆͆̃̌̇͜w̵̨̗̗̙̺̳̯͇͚̻̝̆́̅̒̋̍̓̉̕͜į̸̖͍̮̥̹̲̄̓̀͘͠l̷̛̯̩̹͓͕̤̭̤̼̃͋̐̾̾̔͌͠ͅl̸̢͎͚̫̩̣̯̥̞̙̈͜͝ ̵̛̼͚͖ǫ̶̭̲̳͈̺͕̯̑̌̿̀̈̇̋̏̊͑̈́̎̏͝b̷̲̲̹͈̬̞̩̯̦̣̗̣̿̉͌͜ͅͅé̷̖͔̲̼̱̯͕̫̺͓̱̽̀͒̽̕ẏ̵̨̡̡̻̝̬̘̠̮͇͕̹̺͊͂̈́̽͊̈́.̸̧̨̧̧̛̛͇̣̖͍̣̰͙̳̟̬̠̃̽̏̊̀̒͌̚ ̵̖͔͔̙̑̔

Celestia's eyes turned black for just a second, unnoticed by everyone except for Flurry Heart and Spike, who felt their spine shiver upon seeing it. Their bodies had frozen up as they thought only one word entered their minds when they saw those eyes: Evil.

"I'm fine!" Celestia snapped before rubbing her head with her wing. "I'm fine. Just...a headache. I agree with Twilight. We need to use the cannon."

"I have everything prepared," Twilight said as she nodded. "I just need the Elements of Harmony, and I can have it all ready by tomorrow."

"Very well," Princess Celestia said with a nod. "This war needs to end before more lives are lost. We shall test this Harmony Cannon and see what can be done with it."

"I...I don't..." Pinkie Pie's hair began to deflate as she quickly ran out of the room, much to the surprise of the others. Rarity, Rainbow Dash, and Applejack all rushed after her while the others just stayed in the room. The Princesses began talking to each other about the plans to use the canon while Flurry Heart and Spike stood apart from everyone else.

"...You saw it too, didn't you?" Spike asked with terror in his voice.

"I did," Flurry Heart whispered as she looked ready to cry. "I never... I never felt so scared..."

"I've seen the eyes of some of our most terrible villains in the past, but never before have I felt pure evil like that," Spike said as he stared at Princess Celestia, who seemed to be none the wiser of what just happened. "What do you think is really going on?"

"I don't know...I just know that this is wrong..." Flurry Heart whispered as she looked down at the ground, much to Spike's surprise. "I don't like the war. I hate the war. Always have. I thought humans were cool and interesting, but I had to keep it a secret because Mom and Dad didn't like them. Not to mention how Auntie Celestia, Luna, and Twilight are about them. I think this whole thing is so stupid and...and...I lost my Dad because of it."

"What about the humans who killed your father?" Spike asked.

"How is my grief any different from all the other human children who lost their parents?" Flurry asked with a snort. "I miss my Dad. I want him back, but I'm not the only one who lost somepony in this war. None of them would be dead if we didn't just have this war in the first place. A war we started."

Flurry then tearfully looked up to Spike. "So who's really at fault? The ones who were defending themselves or the ones who started it all in the first place?"

Spike said nothing, but slowly he hugged his step-niece and let her sob on his shoulder.

+}{+

Needless to say, the other Elements were very hesitant about letting their Elements be used for such a thing, but in the end, they were ordered to do so by Princess Celestia.

At the top of the fortress, the Harmony Cannon stood ready as the final preparations were being set up. Twilight was by the control console while the others all stood to the side.

Spike had tried once again to get through to Twilight, but he failed. He kept Flurry Heart close to him while watching Princess Celestia, staring at the cannon with a stoic expression. Flurry Heart wasn't the only one with bad feelings about the war. He, too, was against it but kept himself silent to support his family.

Now I don't even recognize them, Spike thought to himself as he stared at his sister in all but blood. The loss of her brother, the humiliation at the hooves of The Doctor, Fluttershy and Discord's betrayal, and the trauma she went through upon losing her eye and wing had drastically changed Twilight and not for the better. She wasn't even there to help her parents deal with Shining's death, ignoring them and everypony else just to focus on the war.

"Everything is ready," Twilight said as she turned to the others. "However, I'll only fire this if my fellow Princesses agree with this."

"I don't agree with this!" Flurry Heart said rapidly, but Twilight glared at her.

"I mean official princesses," Twilight said in such a tone that it made Flurry wince.

"Twilight! Don't talk to your niece like that!" Cadence harshly shouted as she growled. "Fire it if you want, but don't act so cold to your family!"

Twilight's expression softened as she sighed. "I'm sorry, Flurry and Cadence. I'm...just a bit stressed."

Princess Luna closed her eyes and shook her head. "Fire it. I don’t like it but as you said, we have little options if we are to win this war."

Princess Celestia nodded as well. "Do it, Twilight."

"Very well," Twilight said as she pushed a big red button and stepped back.

+}{+

"Ugh! Even when I'm in a new body, I still cannot get used to the taste of carrot juice," The Doctor said as he put the glass down and wiped his mouth. "Thanks anyway, Carrot Top."

"Eh, it was worth a shot," Carrot Top said as she took the glass and walked over to the other side of the TARDIS's main room, where Derpy, Discord, Flash Sentry, and Lyra were all playing cards. "So who's winning?"

"Me! Full house!" Flash cried out as he put his cards down.

"Tch, three of a kind," Lyra grumbled as she tossed hers away.

"Straight," Discord grumbled as he summoned a glass of chocolate milk and ate the cup. "I still don’t understand why you won’t let me deal."

“Has it ever occurred to you that it's because the cards keep talking every time you do?" Lyra pointed out with a raised eyebrow.

"Guess I win the pot!" Flash Sentry said as he was about to grab his winnings on the table when Derpy played her hand and made him drop his jaw.

"Straight Flush! I win!" Derpy said as she took the chips and began to add them to her growing collection.

"Son of a..." Flash grumbled and crossed his arms before pouting. "Are you sure you're not cheating?"

"Nope! I'm just lucky," Derpy said with a giggle.

"She's not lying," Carrot Top said with a snort. "One time, I took her to Las Pegasus, and she won over four hundred thousand bits at the slot machines in an hour."

"The hay?! What did you do with that money?!" Flash asked in disbelief.

"I spent it all on a special lifetime supply of Mama Goodies Muffins!" Derpy answered with a bright joy as she rubbed her stomach before pouting. "Too bad they're no longer around."

Suddenly, a loud buzzer came from the TARDIS console, which made everyone jump. The Doctor started to turn pale as he rushed over and started working on the controls, looking more frightened the more he went to work. The others rushed over but made sure to give him enough space so he could work without interruption.

"What's going on?!" Lyra asked with worry.

"The TARDIS detected a large spike of energy. According to these readings, this is...no...it can't be...it wasn't supposed to be discovered like this...it's way too soon," The Doctor whispered in horror.

"What is it?!" Flash asked, looking more worried the more The Doctor behaved.

"Hey! What's with the alarm!" Dinky shouted as she and Fluttershy rushed into the control room. "You can practically hear all over the TARDIS!"

"The Doctor says some kind of energy is building up," Carrot Top answered.

"What kind of energy?" Fluttershy asked with worry.

"...H.E.P." The Doctor answered as he began working even faster. "In your original timeline, you went to war with an alien race known as the Prethoryn Scourge. They were a bio-organic intergalactic hive-minded race with the only objective: infesting and consuming the galaxy. Entire star systems fell to them, and while the Shadow Proclamation was the main force destroying them, Equus at the time was caught up in its invasion as well. It was a devastating war that pushed you to the brink until the invention of the H.E.P."

"H.E.P?" Discord asked, tilting his head.

"Harmonic Energized Plasma," The Doctor answered, which made their eyes widen. "After the creation of The New Elements of Harmony during The United Equus Republic's Civil War, there was a new order for specialized creatures to defend your borders from all threats known as the Guardians of Harmony. Each was a unique super soldier that had a small piece from one of the twenty-two New Elements-"

"There are six Elements," Lyra pointed out.

"At the moment. You'd be surprised how many virtues were made into new Elements over time," The Doctor said before continuing where he left off. "The pieces were fused into the bodies of the Guardians which, combined with bioengineering, nanotechnology, and cybernetics, created one of the deadliest special forces in the universe. But even they were still struggling against the Scourge. Until they discovered a means to combine harmonic energy with their elements in combination with a unique plasma formula.

It's a pure weapon of mass destruction that helped the Republic win the war but at the cost of having to practically melt their planets due to the Scourge infestation being so bad that they had to completely destroy their settlements just to cleanse them."

"And that energy is being used right now?!" Lyra screamed in horror. "Something that can wipe out entire planets?!"

"Nothing like that. The energy isn't that big, but the build-up is concerning. I'm amazed it was made this early to begin with!" The Doctor shouted in anger. "How the heck could this have been found?! Obviously, it's from Equestria, and the theory wasn't that hard to come up with, but even so, it would require the Elements of Harmony and a brilliant mind to-"

"Twilight," Discord and Fluttershy answered at the same time.

"...Yes, it has to be her," The Doctor sighed in anger as he shook his head. "Unbelievable. One of the most brilliant mares in the universe, and this is what she's reduced herself to. A mare who revolutionized the entire world during her Golden Age is now a monster."

"Look, whatever she did, do we know what she's doing?!" Lyra demanded.

"Well, the energy is coming from somewhere in the Crystal Empire, but the way the readings are showing..." The Doctor then went dead silent as his entire body froze. "Oh no..."

"What?" Dinky asked as the others waited.

"...Oh no, they wouldn't...."

"Doctor, what is it?"

He slowly turned to them and looked at them with such sorrow that his words were like hearing the living tone of the tragedy itself.

"I'm... I'm so sorry..."

+}{+

At that moment, a large multicolored beam sailed through the sky.

It sailed and arced itself from the Crystal Empire to the direction of the upper east area of the United States of America. Humans and ponies looked up and saw the arc sailing above them. Military systems only had a few minutes to sense the energy before it landed on its target in Cambridge, Massachusetts.

From space, watching from their space stations, astronauts of the human race watched in horror as a bright explosion emitted from a small area on Earth and grew. From Massachutsetts, did the explosion of bright lights spread like that of a growing infection without end. People just going about their day soon found utter oblivion before they knew it.

The entire states of Massachusetts, Vermont, New Hampshire, Maine, Connecticut, Rhode Island, Pennsylvania, New York, Ohio, Lower Michigan, and half of upper New Jersey were wiped out. Even Canada was not spared as Toronto, Ottawa, Montreal, and its surrounding areas were hit as well as the entire regions of Nova Scotia, New Brunswick, and Prince Edward Island.

Cities vanished from the Earth, and nothing was left behind but utter ash and the smell of death. From Chicago to Cape Breton Island was nothing but a large and silent aura of pure heavenly light that eradicated all life in its presence.

When it finally settled after twenty minutes, eight-five million lives were gone.

It was the single greatest tragedy in human history.

+}{+

What have we done? That was all Rarity could think in her mind as she walked through the quiet town of Ponyville.

It had been three days since they fired the Harmony Canon, and Rarity could barely remember what had happened afterward. She remembered coming home to her husband, crying her eyes out, and passing out later when she heard the news of the casualties.

Eighty-five million.

Eighty-five million humans, and ponies living in their areas, were dead.

And she played a part in it.

Her Element, Generosity, was now Genocide in her mind.

She had given it to Twilight, who looked satisfied with the results in the end, and she let it be used so that it made her feel nothing but self-loathing. Rarity couldn't even look at herself in the mirror without smashing it now. She didn't know what she looked like, but whatever ugliness on her face was nothing compared to the ugliness she was feeling inside.

All of them had been affected when they heard the results: Applejack threw up, Rainbow Dash was so pale she nearly lost all her color and Pinkie Pie? She fainted. Honest to Harmony fainted, and it took hours for her to wake up. She just ran back to Ponyville, nopony stopping her.

She didn't know what Spike was thinking, but he was said to have had an argument with Twilight that resulted in them yelling profanities with each other. So he clearly didn't agree with what had happened either.

What have we become? Rarity wondered to herself as she continued to walk throughout the town. We were just friends and occasionally heroes, but now? We're monsters. Fluttershy was right. Lyra was right. Discord was right. This war? This isn't right! It's... it's wrong.

Rarity then paused and looked at the silent house of Sugarcube Corner.

The Cakes were out on a family reunion with Pinkie Pie to look after the place, but nopony had seen her in days. The store remained closed, and no matter who knocked, there was no answer. Rarity knew Pinkie Pie had to be taking this bad.

No, she has to be taking this worse.

Being Pinkie's friend, she was one of the few who knew where the second key was and took it out of the potted plant nearby before unlocking the door. She opened it, only to find the place dusty and dark. "Pinkie? Are you there? It's me, Rarity."

There was no response.

"Darling, I...I wanted to check up on you..." Rarity said as she walked in and closed the door behind her. The silence was unnerving. It was so unlike Pinkie Pie to keep the house quiet. She wondered if she was up in her room and walked up the stairs as quietly as possible just in case her friend was sleeping.

When she arrived at the door marked with Pinkie Pie's cutie mark, she knocked on it only to notice the door was slightly open. "Pinkie?"

When Rarity opened the door, she froze for five minutes before screaming.

Pinkie was hanging by a rope around her neck and a nearby knocked-over chair under her. Her eyes were wide, and her pupils dilated with her mouth wide open while her dried tongue stuck out as a fly landed on her face without twitching from the muscles. Her long pink hair was dull and a tombstone and lifeless as her corpse.

There was only one note left behind next to the chair:

"It isn't funny anymore."

Author's Note

What the Jumbled Text says:

"I command you. You will destroy all you can and cause chaos in my name."

"You hate them. They killed your daughter. They will kill your family. You must destroy them before they destroy you. You will destroy The Doctor."

"I am so close. Close to achieving my goals. The Doctor must not stop me. You will obey."

And at last we have caught up from where Regeneration was on Choice. Next week I shall post Regeneration Part 9 which I've worked on since I started posting the chapters. Need to work on Part 10 when I can.

As always, please help out at the NegotationsVerse TV Tropes Page. We even have a Regeneration Focus section: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 9

"Every great decision creates ripples, like a huge boulder dropped in a lake. The ripples merge and rebound off the banks in unforeseeable ways. The heavier the decision, the larger the waves, the more uncertain the consequences."

- The Seventh Doctor

+}{+

The words "Pinkie Pie" and "Funeral" should never be in the same sentence. Especially together. It sounded wrong to think of such a thing even happening. Pinkie Pie was special. Not just in how she made everyone laugh and smile but in everything she did, from appearing out of nowhere to sensing events before they occurred. Rainbow Dash wasn't an idiot. Everypony had to die someday, but Dash always figured that Pinkie Pie would die of old age while outliving practically all of them, with her wake being a big farewell party.

Only Pinkie Pie was the first Element to pass away and in the middle of her prime.

The funeral was the most somber and depressing thing Rainbow Dash had ever been to; not only did she feel like she would never be happy again, but it felt like a disgrace to everything Pinkie Pie was in her memory. There were no balloons, happy, colorful flowers, or uplifting songs. Even the memories of her were spoken in a dark, tearful silent mood.

The reasoning was simple. Nopony could come to terms with it. Because it just seemed so unfathomable and wrong that the word couldn't even be muttered.

Suicide.

Of all ponies, the Element of Laughter itself, Pinkie Pie had killed herself. Hanging her neck by a rope that suffocated her to death until she was nothing but a corpse. Rainbow Dash had heard Rarity screaming at Sugarcube Corner and rushed in, thinking she was in danger. When she saw Pinkie's dead eyes and realized what had happened, Dash threw up and panicked. Something she had never had in her entire life. Rarity, meanwhile, had practically torn Pinkie Pie off her hanging spot and tried to do CPR, screaming at her to wake up.

But she didn't once breathe or move again.

It took four ponies to finally get Rarity off the body so that the body could be taken away to the hospital's morgue with a doctor to help calm Rainbow Dash down.

Rainbow Dash, standing in the rain with her friends by her side, watched as the pink casket decorated with flowers and cards was lowered into the grave after final words from a somber Princess Celestia. The entire graveyard was filled with ponies from practically all over Equestria. All of whom were touched by Pinkie Pie in some way. All who wanted to say their farewells. Rainbow Dash barely dared to touch the casket or say anything. She was only thankful it was a closed service since she couldn't even imagine the thought of seeing Pinkie Pie lying in there as cold as a statue. Applejack and Rarity were by her side, looking just as staggered as her. Rarity hadn't been able to stop crying, and AJ barely said a word, instead looking downward to the point her hat covered her face. Everypony was sad, and not one smile could be given. Even the unemotional sister, Maud, hadn't stopped crying silently since the service started.

When the sound of the casket hitting the bottom of the hole was heard, everypony started to turn away and return home. There should have been some kind of party or celebration for Pinkie's life. But nopony had the strength to do one. How could anyone have a party when the premiere party pony was gone?

Rarity and Applejack were already leaving to be with their families. The only ones remaining in the graveyard soon were Dash, the gravediggers, and Twilight Sparkle. It was taking all of Rainbow Dash's strength to not rush over to Twilight and smash her hooves into her face. Because the damn alicorn hadn't cried or shown any sorrow during the funeral. She gave a speech and said she would miss Pinkie while stating she loved her, but Twilight did it with such a stone-cold expression that either Twilight was hiding all her emotions inside of her or she was not feeling anything. Rainbow Dash wanted to believe it was the former, but ever since she returned from Osaka, something had clearly changed Twilight, and not for the better.

The damn Harmony Canon was proof of that.

Rainbow Dash was no stranger to killing. She had done so in the war against humanity. But when she learned what had happened in the aftermath? All the lives that were just snuffed out like that? Rainbow Dash finally felt something that she had never felt for any human before: sympathy.

Rainbow Dash still couldn't sleep well and drank more often than usual. Her Element had caused one of the worst acts of mass murder that had ever happened both in Equestrian and Human history. To make matters worse, many ponies hated Equestria's princesses and heroes for what they had done and outright called them monsters. They finally went too far to the point that areas of the nation were outright rebelling or seceding from Equestria out of disgust and horror.

Ponies were outright calling the Elements of Harmony the Elements of Massacure for their actions.

And Rainbow Dash couldn't find it in her to deflect that.

War was one thing, but this was wrong.

So wrong that Pinkie Pie took her own life because of it.

Seeing the casket for the first time, Rainbow Dash finally understood why ponies had defected. Why other ponies rejected their "mission." And why Equestria was tearing herself apart to the point that you might as well call it the prelude to a civil war.

This is wrong, Rainbow Dash thought as she felt tears dripping down her eyes. What have we done? What have I done? I...I want...

She wanted the war to end.

She didn't care about anything else anymore.

She just wanted all the death to stop.

And yet she didn't know how to do so.

Save for one way, she knew how.

"I'm not letting you use my Element again," Rainbow Dash said to Twilight, who turned around and narrowed her eyes. "I know Rarity and Applejack already told you not to use theirs, so here is my statement. It's not going to be used for your Harmony Canon. Never again."

"Dash, we need-"

"We need to end the war, Twilight, but not like this. We need...to stop this," Rainbow Dash stated while noting with bitter irony how it was coming from her of all ponies. She had called out Lyra for thinking this way before she went on the run. Now she was telling Twilight to end a war that had gone out of control. "Half of Equestria is either rebelling or will rebel. I can't even sleep without thinking about the devastation we caused. And Pinkie Pie..."

Rainbow Dash took a deep breath before pointing to the grave. "Pinkie is dead."

"...I know, Dash," Twilight whispered as she closed her eyes. "I know she's dead. But that's not my fault."

"She's dead because you made us into monsters!" Rainbow Dash screamed.

"None of you refused to give up your Element in the end," Twilight said, looking directly at Rainbow Dash in the eye. "You gave me your elements and we used them. You could have said no. All of you could have said no. But you didn't. I told you everything possible with the Harmony Canon, and you still went with it anyway. As did the rest of the Princesses."

"... You're right," Rainbow Dash said with a heavy sigh. "I did. I didn't think it would be this bad. Maybe this was the wake-up I needed to finally understand what Lyra was saying about the war. Because this isn't us. This isn't supposed to be us, Twilight. I thought we were doing the right thing with the war because humanity really needed our help, but after what happened? I finally realized they do need help. Help from us."

"What you are speaking of is treason, Dash," Twilight pointed out.

"Then bucking arrest me. Because I don't give-to use a human term-a fuck what you think, Twilight," Dash growled as she stomped her hoof. "We just lost Pinkie Pie. Pinkie Pie! One of our best friends! And here you are not even sad-"

"Don't you dare think I am not sad, Rainbow!" Twilight hissed as she closed her eyes. "You think I'm not horrified that she killed herself? That I lost one of my best friends? That, every night, I don't cry thinking of all the times we were together? Do not accuse me of not caring because that can't be the furthest thing right now. I am just keeping calm because if I don't..."

There was a long silence between the two as the rain continued to fall on them. If the grave workers were paying attention, they kept silent about it. Twilight sighed and opened her eyes, looking more tired and lost than Rainbow Dash had ever seen her friend. "My brother is dead. My parents are still unable to come to terms with it. Fluttershy, Flash, and Discord betrayed us. Spike refuses to talk to me, and our last conversation led us to say things that both regret. Princess Celestia has been keeping to herself in her room for days. Princess Luna is too busy trying to keep things together with me. Cadence is dealing with the same issue in the Crystal Empire, and her daughter refuses to speak to anypony. Half of Equestria is rebelling, and numerous forces are outright going awol and joining the other side. Now my friends refuse to help me or deal with me because of what we all agreed to do-"

"And you want to do it again," Rainbow Dash interrupted with disgust. "Applejack told me you wanted to use the Harmony Canon again."

"Dash, humanity wants to destroy us," Twilight growled as she shook her head. "They already fired six nuclear missiles at us, and if it wasn't for the barrier protecting us, we would all be dead."

Dash winced upon hearing that but couldn't say she was surprised.

"I am trying to do what I can to save our species from not just humanity but our own ponies, who have lost faith in everything we believed," Twilight sighed and shook her head. "Not to mention we still have no solid way to counter The Doctor."

"...Then why bother fighting, Twilight?" Rainbow Dash asked with a heavy sigh of her own. "Look, I hate giving up as much as the next pony. But it sounds like this war will get worse in our favor. What's the point anymore of this? We failed. Can't we just sue for peace or ask for a ceasefire? Damnit, I'll even take going home with our tails between our legs. I just... I can't do this anymore."

"We can't go home," Twilight whispered, shaking her head. "Now that Pinkie Pie is dead, we cannot use the spell. The Elements of Harmony were needed to get us home; we're here for good without them."

"Then let's negotiate with-"

"I will see all of Equestria burn before I negotiate with The Doctor," Twilight growled with such rage in her eyes that Dash swore she saw the build-up of dark magic out the corners of her whites. "You have no idea what he is capable of, Rainbow Dash. What I saw him do. He's the worst enemy we've ever faced, and I fear what he will do to us all if he wins. I will not bow to the stallion that killed my brother, scarred me, and embarrassed me like that. Never."

At that moment, Rainbow Dash knew that the Twilight she knew was dead. Something inside her had broken, and the once kind, sweet mare who wanted to learn about friendship and spread it to the world had been replaced with a bitter and spiteful being filled with sorrow and rage. While Rainbow Dash could blame The Doctor for it, it felt like a moot point. This wasn't the Twilight she loved and cared for. The one she went through so much with in the past. The Twilight that Rainbow Dash respected and loved.

This was a total stranger, and she did not intend to follow her to whatever end was to come.

"Then count me out," Rainbow Dash whispered as she shook her head. "I'm done, Twilight. I won't leave Equestria and do what I can to defend her, but I want nothing to do with you anymore."

"What happened to being loyal, Dash?" Twilight asked in a tone that sounded both accusatory and hurt.

"It's called being loyal to your consciousness, Twilight," Rainbow Dash replied before turning away. "And my loyalty is to those I consider my friends. You aren't the Twilight I am friends with, and I hope she returns to us one day. But for now? I want nothing to do with you."

Rainbow Dash didn't even let Twilight say anything back in return. She just took to the skies as fast as she could to hide the fact that she was crying.

+}{+

When the funeral was over, Applejack just went home, grabbed her hardest drink in her cellar, and went to find a good place to sit and ingest it. Much as a part of her wanted to drink it all down in one gulp and get so drunk she'd be more numb than a mouth in a dentist's office, she sipped it quietly while being deep in thought. Applejack often liked to think she had a clear and leveled head. It came with growing up faster than she wanted when her parents died. So why in the sam hill did Ah agree to let Twilight use mah Element like that?

Applejack would be the first to outright say she disliked humanity. Hay, she might even hate them, especially since Big Macintosh was now a prisoner or dead because of them. But even she knew that what happened with the Harmony Canon was wrong. Maybe because she had never been involved in the war, save for donating to the cause, she couldn't grasp the loss of life. But eighty-five million lives? And partly because of her?

Not even her hatred for humanity could diminish the disgust and guilt that was worming inside her.

Applejack, for the first time in her entire time since the war began, felt that they had made a mistake in what they did. Humanity deserved to be converted, and some may even need to die for how bad they really were. But this? This was wrong.

And it seemed half of Equestria was thinking the same thing. Portions of the entire nation were outright demanding an end to the war or committing secession. Some were even calling for the Princesses and Elements to be judged for their crimes of mass murder. Ponies were defending their actions, citing it was war, and they needed to stop humanity for the greater good of harmony. But this felt like something other than harmony. This felt like the very opposite of it. Applejack couldn't even look at herself in the mirror anymore without thinking of the final moments of all the humans and some of the ponies settled in those areas that died instantly. Others couldn't even look Applejack in the eye because they were disgusted with her despite all she did for Ponyville. More than one pony in Ponyville sneered or whispered behind her back, insulting her good name. Usually, Applejack would confront somepony talking negatively about her, but this time she didn't have the strength to do so.

Partly because she felt, deep down, she deserved it.

Pinkie Pie's suicide only made her feel more justified for her self-disgust. Pinkie Pie was a good-hearted pony. She could see the best in everyone, even the worst of them. For her to just kill herself like that? It meant that she felt that what they played a part in was beyond forgiveness. And Applejack didn't know how to move on from that nor what to even think what this meant.

Was this war really unjustified? Did it mean that Lyra was right? Were the princesses, the being she worshiped her entire life, wrong? Was Equestria the villain? Do Ah even want to believe that, or can Ah even believe that to be the case?

"Applejack?" She looked to her left and saw her sister-in-law, Sugar Belle, walking towards her while still dressed in her funeral dress. "I was wondering where you left."

"Ah needed to think," Applejack answered as she took another sip from her bottle. "Applebloom?"

"In her room. Sobbing," Sugar Belle answered as she sat down next to Applejack. The farmer pony handed her sister-in-law the drink, and she slowly took it before taking a large gulp and giving it back. "I need to tell you something. I...I got a letter from Big Mac."

Applejack's eyes widened, and her head snapped towards Sugar Belle so fast it nearly broke. "H-How?"

"A pony I had never met before handed it to me. I think he was a member of the Underground Railroad," Sugar Belle answered with a sigh. "Before you ask, no. I've never been involved with them. This just came out of the blue."

"Are ya sure it's from him?" Applejack asked desperately. Ever since Osaka, Applejack wasn't sure if her brother was a prisoner or dead. Despite hearing the stories of how humans treated their prisoners, she wanted some hope that her dear older brother was alive.

"I've read his writing so many times in the love letters we always sent to each other that I know his style by heart," Sugar Belle replied before giving a small smile. "He's alive."

Applejack felt her sorrow from earlier slowly diminish as she let out a big gasp of relief. He was alive. Big Macintosh was alive. She hadn't lost another family member like her parents. "W-What did he say?"

"That he was being treated well and believes the war is a mistake," Sugar Belle said with a heavy sigh. "He says he's had time to learn about humanity. See their side of everything. He believes that...Equestria needs to stop before we do something we'll all regret. After what happened with the Harmony Canon, I think it's too late."

Applejack didn't say anything but grunt a bit.

"He...he told me to leave Equestria," Sugar Belle admitted as she closed her eyes. "Told me how to contact the Underground Railroad, and they could get me out. He wanted me to get you and Applebloom out as well."

"...That would mean leavin' the farm," Applejack whispered in disbelief. "Leavin' Ponyville. Mah friends. Equestria. He wants us to just...drop it all and go?"

"Applejack, the writing is on the wall," Sugar Belle said as she got up and glared at her. "We just committed the biggest war crime in history that I can't even blame the humans for wanting to nuke us at this point. Half the population is ready to outright rebel to end the war or fight them with fanaticism because they think they are traitors. You can't even look Twilight in the eyes, and Pinkie Pie is dead while Fluttershy has already left with Discord. The humans are winning the war, even if they haven't managed to attack us directly. It's almost a matter of time before they figure out a way beyond the barrier. They already figured out a way to undo the Conversion Potion. How long do you think it will take until they get past that?"

"But..."

"Applejack, the moment the barrier goes down? Equestria is finished," Sugar Belle stated with a shake of her head. "I love my home, but I love my family more. I love Big Macintosh, and I'd rather live with him in the human world than waste my time preparing to suffer or die in a land that has lost all sanity. The only reason I am telling you all this is that you and I are family. I love you and Applebloom, and Big Macintosh misses you both. Come with me to see him, and we can put this entire war behind us. Let Equestria just suffer for the madness it created. Let's just get out of here, please."

Applejack, on her part, didn't say anything. It was known that there had been some ponies in Ponyville who had defected to the humans. Ponies that Applejack had known her entire life or for a long time that she felt disgusted about for leaving like a bunch of traitors. She called them all sorts of names and swore that if she ever learned that a pony was thinking of betraying Equestria for the enemy, she would tell the E.S.S. as soon as she could.

Now Sugar Bell, part of her family by marriage, was telling her outright that she wanted to defect. There was a part of Applejack that told her to do this. To take all of them and abandon Equestria as if she was a sinking ship with too many holes to plug in.

The other part of her was telling her to tell the nearest E.S.S. agent or one of the Princesses that her sister-in-law was planning to leave Equestria with an organization deemed an enemy of the state. It hurt Applejack to hear Sugar Bell say she would rather be with the humans than her own kind. It hurt even more upon realizing that Big Macintosh was telling her to do it, meaning he had the same mindset.

Like Applejack, Big Macintosh was proud of their home and all they accomplished with it. Four generations of Apples had made Ponyville the place it is today, and a legacy was tied to it. To give all of that up? Big Macintosh would never suggest such a thing unless things were really that bad, even under the threat of torture.

But if they did this, it would betray everything Applejack stood for.

Applejack closed her eyes and lowered her head. "Take Applebloom and go."

"Huh?" Sugar Belle asked with a surprised expression.

"It will look suspicious if all three of us leave," Applejack said before taking another drink. Wiping her mouth, she continued, "Ah'll tell everypony that you took her to see your relatives down south. Ah'll then say Ah got a letter sayin' ya both died in an accident or something. Maybe them Underground Railroaders can arrange that. Just...take her and go to Big Macintosh. Make sure ya don't come back until this war is over. If there is anythin' to come back to."

"B-But what about you?" Sugar Belle asked.

"Ah'll stay here on the farm," Applejack whispered, slowly getting up and stretching her legs. "Ah can handle things here on mah end."

"Why can't you come with us?" Sugar Belle asked, biting her lip.

"Because Ah can't leave Equestria. Or Ponyville," Applejack chuckled with a shake of her head. "Ah'm stubborn. What can Ah say? This is mah home and, come hell or water, ah gotta stay with her. Even if she's wrong, Ah just can't leave her, but Ah won't let y'all stay here with me. So go. Take Applebloom. Get back with Big Macintosh. And..."

"Y-yeah?"

Applejack shook her head. "Pray that things don't get worse."

+}{+

Cadence swore long ago that she would never be a heavy drinker. She owed it to a mistake in her youth when she and her friends at school decided to drink despite being underage. It led her to do some pretty stupid stuff while drunk that made her get the biggest grounding she ever got from her Aunt Celestia. Since then, Cadence swore she would never drink again.

The past half year had seen that promise break apart into tiny pieces. Cadence's husband died, and her sister-in-law was battling PTSD and pushing everyone away. Humanity was winning the war with numerous subjects under her command and care dying regularly. There were outright protests and demands to end the war from within the Crystal Empire, with even talks of overthrowing Cadence and seceding from Equestria to be their own nation again. The final stroke that broke the camel's back was the Harmony Canon. Deep down, Cadence had wanted to use it to get revenge for Shining Armor's death. To make the humans pay and have them feel the pain, she felt deep inside. Especially if they were lucky and wiped out The Doctor as well.

But when she learned of the devastation and the harm it had caused, Cadence had never felt more disgusted with herself in her entire life. That was the first time she ever had an all-night drinking barrage in private to deal with the sorrow and pain in her heart. Learning about Pinkie Pie's suicide was all but the assurance that she needed to know this was wrong. Twilight's friends were like family to Cadence, even if she only got to know them during and after her wedding. To lose the Element of Laugher from suicide of all things?

It was like nothing would ever be the same again and that even if they won this war, it would be a hallow victory.

Although right now, war was the furthest thing on her mind.

The relationship with her daughter was the primary one.

Since using the Harmony Canon, Flurry Heart had refused to look or speak at her. Cadence knew she was upset about allowing it to be fired, especially when she made it clear that she was against it. Flurry Heart's expression was not sorrow or anger but disappointment when fired. At everypony there that day except for Spike, who had a fight with Twilight that seemed to end their friendship for good. That had also been heartbreaking as Spike and Twilight were always together, the best of friends, and were practically family in the eyes of the other. For him to reject her like that, it also had to be painful for him.

My whole family is falling apart, and I can't do anything, Cadence bitterly thought as she slowly got up from her bed and looked down from her balcony at the Crystal Empire. I can't even maintain order in my own kingdom.

Numerous riots happened in the city in the following days. It almost prevented her from going to the funeral. The Crystal Ponies had finally had enough, and most of the city was demanding that Princess Cadence end their involvement in the war, or they would force her out and restore their independence. The only thing keeping her safe from an outright revolution was that the military and guard were still loyal to her and her husband's spirit. Even if some of them didn't look at her with happy eyes anymore.

It was so bad that even Luna was telling her to get out of there with Flurry Heart until they could take back the situation under their control, but that was just one of many problems Equestria was facing. Most, if not all, of the southern lands, had declared independence, with lands on the east and west split over ending the war. Some were even demanding the princesses step down. Only the core and northern lands, save for the Crystal Empire, were still showing absolute loyalty to the point that anyone saying even the slightest criticism was being dragged out of their homes by angry loyalists and handing them over to the E.S.S. Some hangings were even being done.

Have we really fallen so low? Cadence wondered as she recalled Discord and The Doctor's words to her, Twilight, and Shining that day in Osaka. About how far they had disgraced themselves and become blinded by their own arrogance, they couldn't see what they were doing was wrong. Cadence believed in Celestia's words about humanity. She never lied to her or told her anything that made her think her aunt was manipulating things.

But for the first time, she began to doubt.

Was humanity really so evil that it warranted all the extreme measures being used to fight them?

Was the war really nothing more than a cover-up to create a pony-only world by effectively wiping out a species that had ruled it on its own for one reason or another?

Was their world really...gone?

"Your majesty!" A guard screamed as he burst through the doors, nearly scaring Cadence into jumping into the air. "Princess Flurry Heart has run away!"

"What?!" Cadence shouted in shock and horror as she teleported to her daughter's room. She looked around and tried to find any sign of her, but there were nothing but worried guards and staff members as one was reading a piece of paper. Fear gripped her heart as she snatched it from him, and her worst fears came true upon reading it.

Dear Mother,

By the time you read this, I am already out of Equestria and heading to the human lands with Spike. I don't do this without regret because I know I am leaving you and others we love for siding with our supposed enemy. But I have had enough. I am not going to sit by and let you all commit genocide on a species that Celestia hates for whatever reason that, to Spike and me, is not good enough to warrant the destruction we are bringing.

I have had enough. I am defecting.

A war started because humanity wished to decide its own destiny. Yes, I know humanity played a role in my father's death, but how many children like myself have lost their fathers, mothers, siblings, and friends because of this war? Humanity may be flawed, but so are we. We claim them to be the barbarians of war and death, and yet, after seeing what the Harmony Canon has done, I feel that it is more associated with us.

I have always felt that this war is wrong, and Spike does too. We have never said or done anything about it because you, Aunt Twilight, and everypony else are our family. But this has gone too far. Aunt Twilight is no longer the happy and wise mare I love so much but a monster consumed by revenge and hate. Aunt Luna is too blinded by making war and protecting Equestria that she doesn't see that the only ones we need protection from are ourselves. Celestia is mad. Pure mad and zealous in her hatred for humanity. And if the rumors of her leaving our world behind are true, then she is also a monster and a liar who deserves to die for what she has done.

And you? Mom? I love you. And I will always love you. But ever since Dad died, you've been so consumed with his death that you've forgotten all reason. I can forgive forgetting about me at times because of your grief for losing Dad. I know I have as well. I hope this helps you see the light and become the Mom I love again.

Because this has to end.

I think a quote from the human world fits with what I am feeling right now: "Evil wins when good men do nothing."

I have done nothing in the past, probably because, due to my age, I was not expected to do so, but I will do it now. I will stop this war even if it means working with the stallion who helped kill my father.

Because Dad always says you must follow your heart to do the right things.

And it's time I did that.

I love you, and I hope we can still be a family when this war ends.

Love, Flurry Heart.

Author's Note

Definitely a few changes from canon, huh? As always, please help out at the NegotationsVerse TV Tropes Page. We even have a Regeneration Focus section: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 10

“I’ve seen worlds destroyed, civilizations choked in their cradles, whole races fleeing in terror. I’ve seen centuries of art, of science, wiped out in an instant. I just saw a beautiful rainforest burn along with every creature in it. I didn’t even know the planet’s name! If you’re prepared to accept that much collateral damage to the rest of the universe, then what exactly are you fighting for? I’ll protect those with no choice in the matter, no voice.”

-The Eighth Doctor

"I don’t make threats. But I do keep promises."

- The First Doctor

+}{+

When Lyra heard that several nations had fired nuclear weapons at Equestria, a small part of her cheered for it. It was only after the reports of it failing that she felt sick of what she felt and nearly threw up. It was something she never wanted to feel again when it passed, but the unicorn understood why she felt that way. Why, for one moment, she wanted to see her home destroyed in a nuclear fire for the crimes it had committed. Lyra knew there was a massive loss of life with the war and how it went on, but seeing so many lives die in one blow was beyond explanation.

There would be no forgiveness for this, not for any of them. Even Lyra couldn't help but be disgusted for being a pony because of what the so-called "Harmony Canon" had done. She wasn't the only one either, as the massive reports of violent insurgency in Equestria made it clear that at least half the nation had finally woken up to the fact that they were the villains. It was far later than Lyra had hoped, but she supposed it was better than nothing. Diplomats from all over the rebel areas of Equestria were asking to join in revolting against the Alicorns and their loyalists. They didn't care if humanity occupied them or if Equestria became a militarized zone. They just wanted to stop this madness and were willing to repent in any fashion.

Most of the human race and its leaders were close to telling them to go to Hell until The Doctor contacted all the prominent leaders of the U.N. and offered a promise. He would end the war in less than three months, and if he did so, they wouldn't commit a massacre that they would regret years, if not generations, down the line. Considering all he had done for them, they gave him a chance. So far, the Doctor merely asked for time alone in his TARDIS. Everypony else was just waiting for him, but Lyra had enough of that. She needed to do something—anything—instead of waiting around.

Walking down the hall in the hotel room they were being given in Geneva, she paused until she knocked on the door that was supposed to be The Doctor's room. Even after hearing no answer, she pushed the door open with her magic to find the TARDIS open and waiting. Walking inside, she didn't see the Doctor until she noticed him by the tea set table, a cup in hoof while focusing on the TARDIS control panel.

Slowly walking over, Lyra cleared her throat. "Hey."

"Hey," The Doctor muttered, not looking in her direction. "Need something?"

"I was just...wanting to know what you were planning?" Lyra whispered as she bit her lip. "And see how you were doing."

"I should be saying that to you," The Doctor whispered as he sipped his tea and got up. Dusting himself off, he looked at Lyra with sympathetic eyes. "I should have been there to help you and the others deal with this. I know this isn't easy-"

"Easy? It's bucking horrible," Lyra grumbled as she did her best to focus on not crying. "My homeland just ended the lives of eighty-five million humans, and some of them were even ponies. They just committed an act of genocide. I knew some of those ponies who gave the order. One was my fillyhood friend from Canterlot, whom I used to joke around with when we were fillies. The other babysat my friends and me when we were younger. I used to admire Princess Celestia and Luna as if they were idols to be worshiped or loved. I saw the Elements of Harmony as heroes. I loved my homeland even if it was faulty at times."

It took a moment for Lyra to realize that she had failed to hold it in and was crying. "And I just saw that place I was born in perform an atrocity that will never fade away from my memory."

The Doctor slowly wrapped his hooves around her and let her cry. She sobbed and felt the last of her innocence fall apart in his hooves, and she knew the others weren't any better. They all were like this to some degree, and it hurt knowing that things had come to this. To go so far beyond the point of no return that if humanity was to wipe out all of the remaining life in Equestria, she wouldn't blame them for it.

"I know what you are feeling," The Doctor whispered.

"How?" Lyra asked, almost bitterly.

"...Because my species has done worse."

Lyra's eyes widened as she slowly looked up at him and simultaneously saw eyes of pure sorrow and hatred. "The sad truth about the Time Lords is that, despite all the good we have done and the greatness we have achieved, we are not so above all the so-called "savage" civilizations that some higher-ups look down upon. We've committed acts of such cruelties that I won't begin to describe them. Much as Time Lords are respected, they are also feared and hated by the other races in our dimension. I am not above this even."

"But... you've done so much good," Lyra whispered in awe.

"And yet so much death happens because of me or around me," The Doctor sighed as he walked towards the TARDIS controls, with every step heavier than the next. "I've seen so many losses of life, numerous planets become lifeless husks, civilizations wiped out, galaxies burn, empires fall, and even universes crumble, and yet it never gets easier. I personally have wiped out species and destroyed planets. Even got the title Destroyer of Worlds by some, and yet it's fitting. For all I do to save and heal, I am equally responsible for so much destruction and death. Sometimes I want to just run away from it all. Sometimes I just want to stop and never look back."

"So why do you do it?" Lyra asked curiously. She couldn't even begin to fathom living such a life, even if it was as exciting as The Doctor's.

The Doctor turned to her and walked over before using his hoof to wipe away her tears. He gave her a small smile and replied, "Because I don't like seeing tears on faces like yours. Someone has to stop the crying. Someone has to be the monster of monsters that protects the children in the dark. Because every time I think of quitting, I realize I can't because it would all be meaningless in the end. All the things I've done and the sacrifices that were made. I can't let them be in vain. I must keep fighting to believe in something I've come to hold dear in my heart."

Putting his hooves on her shoulders, he whispered, "There is good in this universe, and it will win in the end. Even if someone has to come around in a box and give it a good kick in the right direction here and there."

Lyra was quiet for a bit as The Doctor's words came to her and washed over her worries. They were like medicine after a cold, and she couldn't help but smile. "I guess we'll have to be the kickers, then?"

"Yup," The Doctor said with a cheerful grin before clapping his hooves. "Now then! I've got to take down Equestria as part of my deal in a proper time limit with the U.N. to prevent a total massacre. I need one more thing to achieve that plan, but first things first! Taking down the Harmony Canon! We must do that, and first of that first that was talking about which was first, we need to find out where it is!"

"How are we going to do that?" Lyra asked.

"Oh, I'm sure something will show up to push us in the right direction," The Doctor said as he began to push a few buttons on the console.

"How long will that take?"

Before The Doctor could answer, they heard the door to his hotel room being slammed over, and Derpy flew in with her eyes all dazed and breathing heavily. "Doctor! You have to come quick!"

"What's wrong?" The Doctor asked.

"Spike and Princess Flurry Heart are here! They know where the Harmony Canon is!"

Laura's jaw dropped, and she stared at the grinning stallion.

"Well, that didn't take long now, did it?"

+}{+

Flurry Heart had expected to be distrusted for her status not only as a Princess of Equestria but also because of the dragon beside her. Flurry Heart gazed over at Spike while sitting on her seat in the interrogation room that was provided for her. He glared at two human soldiers across from them, who looked nervous upon seeing a real-life dragon before them. During their travels, Spike ensured she was safe and threatened anyone who thought of doing anything harmful, but she assured her honorary uncle could keep his anger in check.

With aid from the Underground Railroad, Discord had helped transport her and Spike to Geneva, where Fluttershy was waiting for them along with another armed escort. She had sent a letter to them saying she wished to defect and aid them in their war against Equestria and proved her sincerity to the effort by giving all the information about the Harmony Canon save for its actual location. She had to have some means to get them to take her in without playing her whole deck.

It had been risky enough to do all this without her mother, fellow alicorns, or the ESS finding out about it. But once she gave this information to their enemies, she knew there would be no going back, and it would be a matter of time before she was discovered. Even if she was Cadence's daughter, she didn't trust Celesia or her Aunt Twilight in their current state of mind to not hurt her. Besides, this was the best way she could think about saving Equestria.

Spike went with her because he felt the same thing, but he was much more vocal about it. Nopony knew what happened in the argument between Twilight and Spike, but it was clear their friendship had all but ended as Spike outright disowned her. She only asked once, and Spike told her: "The Twilight I know and love is dead."

That was all she needed to hear. If Spike, of all creatures, had given up on Twilight, then she was a lost cause.

Flurry Heart twiddled her hooves while trying to calm herself down. On the other side of the room were what were known as "The Doctor's Companions" and a human in the military named Major-General Marshall Highmoor, who was looking at her with a stoic expression. Her fellow ponies, however, were mixed. Discord and Fluttershy were looking at her with sympathy, and it was only them that Spike's eyes showed any real soft emotion towards. Flash Sentry looked at her with suspicion, as was Carrot Top, while Dinky stared at her like a puzzle trying to figure her out.

It didn't take long for the last two companions to arrive, along with the stallion who had changed the war. The same stallion whose actions took her father away from her forever: The Doctor.

Of all the things she expected, she wasn't expecting someone so young and dressed so weirdly. The Doctor took a look at her and smiled warmly. "Hello again, Princess Flurry Heart."

This made Flurry Heart tilt her head. "Um, I never met you."

"Not now, and well...not in this new timeline. But I did during a Zygon Invasion in the two hundred and eighth year of your reign when they tried to make you marry one of their own in disguise to take over the Crystal Empire. Long story. Thankfully, you married someone who wasn't a red sucker-covered alien a few years later. That was a great wedding. Didn't like the cake, though. Coconut cake. " Ugh, so wrong with those two words mixed together," The Doctor said, which only confused Flurry Heart. She turned to Spike, who just raised an eyebrow and shrugged.

Although he was soon given attention when The Doctor also cheerfully greeted him. "Spike! You old dragon! Well, young dragon, but eventually old one! It wasn't long ago that I saw you with Sunny and the others! Back in my previous body! Wow, you really look good. Word of advice? Keep it easy on the diamonds, or you'll get a big belly."

"Um, okay?" Spike said as he shook his head. "Hold on, whose Sunny?"

"Sunny Starscout? Well, she's Twilight's successor. Brilliant girl. Absolutely fantastic pony and leader. But that's not important right now," The Doctor quickly said.

"So you do travel through time and space," Flurry Heart whispered in awe.

"Yup," The Doctor said with a smile. "Want to see how it's done?"

"Doctor? Please hold off showing your little machine for another time?" Major-General Marshall Highmoor sighed in annoyance.

"Right, sorry. Got a little carried away there," The Doctor apologized as he cleared his voice and sat down across from her.

However, Flurry Heart knew she had to get this out of the way before he could open his mouth and held her hoof up. "Wait." He paused. Taking a deep breath. "Before we talk? Before I officially side with you and do whatever it takes to end this war? There is just one thing I have to do."

A split second later, she slapped The Doctor in the face. Everyone in the room had a tremendous outcry of anger, and the human soldiers looked ready to move, but The Doctor halted them by holding his hoof up. He slowly looked at Flurry Heart with understanding as she bitterly wiped her tears and took a deep breath. "That was for my Dad."

"...I understand," The Doctor said with sympathy and nodded.

"Good," Flurry Heart whispered as she took a deep breath. "I'm here because I want to end the war. My mother, Aunt Twilight, and Aunt Luna are all sucked up by Celestia's madness, and I want it to end. Equestria is tearing itself apart, and the actions that we have done against humanity are unforgivable. Even before the Harmony Canon, we've tried to wipe out a species for no good reason other than we were scared of them. I never wanted this war, but I could do nothing, both because of my age and lack of the means to do so. But after what happened with the canon? I am not standing on the sidelines anymore."

With a deep breath, she turned to Major-General Marshall Highmoor and bowed her head. "Major-General, I know this is not much, but on behalf of Equestria's sane citizens, I apologize for the actions we have caused. I know that is not enough, and it will take decades, even centuries, to be forgiven for our actions, but I am so sorry."

"Sorry isn't enough. It will never be enough for what you have done," Major-General Marshall Highmoor growled.

"I know, but I can start at least by helping end this war. And taking out the Harmony Canon is the first means to do so," Flurry Heart whispered as she stared at the Doctor. "But I want just a few things in return."

"Such as?" The Doctor asked, eyebrow raised.

"I don't care what you do to Celestia, Princess Luna, or Princess Twilight. I know that there is no chance for either of them to walk out of this alive when this war is over. While I love them deep down in my heart, they are not worthy of being our leaders and are no longer the aunts I love and cherish. But I want my mother spared. Jail her for life if you must, so long as she lives and I can see her, I will accept that outcome," Flurry Heart said before standing firm. "In return, I will lead Equestria. I will seek peace with humanity and spend my entire reign making up for the sins of my people. I even plan on eliminating the Church of Harmony. I am neither a goddess nor feel worthy to be one if it was true. The same can be said for my fellow alicorns. Especially since the whole Church is based on life."

"What do you mean?" Flash Sentry asked.

"The Church of Harmony was a means to help unite ponies through a belief that those who are alicorns are living goddesses," Flurry Heart replied with a sigh. "I don't know if there is a god, but I am neither one nor anyone in my family. Hay, they're all atheists if you really get down to it."

"Well, I'd like my time spent at church for all those years of my life back now," Carrot Top grumbled.

"Anyway, I plan to rule not as a divine being but simply as the mortal I am. If need be, I will submit my authority primarily to the U.N. and even slowly transition us into a democratic government. But Equestria will need an alicorn to lead her when this war is over if only to help keep citizens calm and orderly."

"I see no problems with that, do you, Major-General?" The Doctor asked.

"... It's up to the politicians to decide, but I think it would be fair," he answered. "What about the Elements of Harmony? They are still a threat themselves because of their abilities."

Upon hearing this, Flurry Heart's and Spike's faces went dark, silent. Sorrow was decorated in their eyes, and instantly everyone knew something had happened. Fluttershy stepped forward with worry on her face. "What happened?! Spike?! What's wrong?!"

"...Pinkie Pie is dead," Spike whispered, and all the light in the room seemed to have gone out in a blink as everyone stared at him. "She killed herself because she couldn't live with the grief of what she had done."

Fluttershy gasped and held one hoof to her heart and another to her mouth. "No...no nonononononononono!"

Her eyes were wide, and her mouth dropped as her wings froze. Her face began to pale as Discord was quickly at her side to help her stop shaking. "NONONONONONONONONOOOO!”

She rushed out of the room, wailing, and Discord soon followed her. Everyone from Equestria stood in shock as the realization of what had just been told to them was still processing.

"...Pinkie..." Derpy whispered as she sat down and began to tear up.

"No..." Carrot Top muttered in horror as she, Derpy, and Dinky wrapped their arms around each other and sobbed.

Flash Sentry cursed and kicked the nearby wall before muttering to himself as he tried to fight the tears. Lyra looked heartbroken and turned away to hide her sobs as The Doctor sat there with a stoic look on his face, but his eyes were glazed with fury and loss. Taking a deep breath, The Doctor closed his eyes. "I'm sorry."

"Don't," Flurry Heart whispered as she shook her head. "You didn't cause it. Of all the things you did, you didn't cause it. We caused it. This war did it. A war that Celestia started and...I don't know what to think of her anymore. I just...I just don't understand how she can be so...insane!"

Spike snorted. "Considering what we saw in her eyes when they turned black, is it a real surprise?"

"...What?" The Doctor snapped his head towards Spike and immediately went to his face, much to his surprise. "Say that again. Right now. Say it!"

"Um, her eyes turned black at one point. Nopony saw it but Flurry Heart and me. It was when we were debating whether to use the Harmony Canon," Spike said as he turned to Flurry Heart and nodded. "She had a headache. She's had them a few times. Her eyes then turned black. Not like night black, but like pure dark black. Like you couldn't see any light in them."

"And they felt so...evil," Flurry Heart whispered. "I've never felt anything like it in my life."

"...Has she been talking to herself?" The Doctor asked, getting their attention. "Acting moody? Seems like she's having a conversation, but nobody is around her? Repeating certain words over a bit? Isolates herself at times and seems off? Is her mood always going off in random directions at times, especially when stressed? And she seems like a complete 180 ever since coming to Earth compared to how you've known her all throughout your lives?"

Spike and Flurry Heart looked at each other before nodding. "Yeah, how did you know?"

The Doctor was quiet for a few minutes before yelling and slamming his head against the wall, much to everyone's shock. "Of course! It has to be that! It would make sense, but if she is, who is it?! Who the blood damn is it?!"

"Doctor?" Lyra asked. "What are you talking about?"

"CELESTIA!" The Doctor shouted as he looked at everyone with his teeth gritting in frustration. "All this time, I've been thinking, why?! Why would Celestia suddenly do this?! Why change direction in attitude and behavior and start his war?! Why teleport all of Equestria towards this universe in a different dimension?! It made no logical sense, and I think..." He started to calm down and began to look calculated. "No, I have to be sure. I have see her. Face to face. It's the only way."

"Doctor?" Flurry Heart asked before he turned to her quickly.

"The location of the Harmony Canon! Tell me where it is! We don't have time!"

"It's in a military base in the Crystal Empire," Flurry Heart said quickly. "Fort Obsidian."

"I know where that is. Hopefully, it's still in the same place last time I visited," The Doctor said before turning to Major-General Highmoor. "Major-General, tell your entire force to stay on red alert and prepare for anything. Something is coming, and I fear it will be terrible."

He then turned to the others. "Flash? Get Fluttershy and Discord and tell them to meet us at the TARDIS. Carrot, Derpy, and Dinky? You can come too, but you don't have to. This will be more dangerous than I imagined if my worst fears about this situation come true."

"I'm coming too," Spike demanded.

"Fine, but obey everything I say. Got it?!" The Doctor ordered with a glare that quickly made Spike back away and nod.

"Doctor?! What's going on?! What's got you in such a fritz?!" Lyra asked with concern. "I've never seen you like this before."

"...Lyra, I fear that there is more to all of this than we were led to believe. There is a secret reason behind this war, one that Celestia doesn't realize, and that we are all being used. There is another player in this war. Someone who has a stake in and benefits from it but has been doing so in secret, and I fear Equestria is how he or she or it is doing so for whatever unknown goal of theirs," The Doctor whispered in both concern and fury. "If this is true, this changes everything."

"Are...are you saying that Princess Celestia is being manipulated? Or mind controlled?" Flash Sentry asked in disbelief.

"You're joking, right?" Major-General Highmoor asked.

"No, because the signs are very similar to mind control I've seen in the past," The Doctor said seriously. "Plenty of powerful races and beings could be behind this. If it is true, mind you. If so, then Equestria is just as much a victim as Earth is, and that someone is seeking to come up on top in a war they orchestrated for whatever purpose known only to them!"

"But who, Doctor? And why?!" Lyra asked.

"...I don't know," The Doctor admitted but growled. "But whoever they are...they are powerful."

+}{+

In a small section of the universe, a single planet unknowingly played essential roles that many species would not understand how or why. This single planet, which laid perfectly between the tiny sun and moon designed only for it and it alone, had survived countless invasions, disasters, and outright apocalypses despite all the odds. Sometimes it was on their own, and other times it was thanks to a particular well-known alien in a blue box whose name was known throughout the known galaxy.

This planet would one day become the center of many critical galactic events shaping the universe in ways that those currently living it would never dream of having. It would be a plant that would change everything.

Only now, it was a husk of death and rot.

One side forever burned dry, and the other frozen in darkness for eternity. Life no longer existed. The last living being, a dragon, had cursed the pony race before breathing its last and died alone, scared, and forgotten on a planet that now served as the tomb for billions.

"Just as planned, of course."

The figure hidden in the darkness of his new lair strummed his talons upon the benches of his crafted throne. Carved out of the very Tree of Harmony ironically. It had long died the moment it was chosen, abandoned its home dimension, and perished with sorrow and grief, knowing it had failed in the end. The entropy, darkness, and death that had come in the remaining years without the ponies moving the celestial objects had slowly empowered him. Giving him the strength to regain a stable form in this universe that he wished to be his at one point, but no longer.

Not when there was a new universe, a fresh and young one, that he could carve into his own image. It had been his most clever plan to achieve ultimate god-like power. More so than he had already, but it would need careful planning. It had taken him so long to regain his strength after his last encounter with The Doctor. He had time to think and plan while also enacting his revenge on him. After his previous attempts to attack the Doctor directly, he thought it best to hurt him instead by taking what he treasured most. This planet and its pathetic people. It was a slow manipulation, but he was careful and patient, if nothing else. Nothing would stop him this time. And not only would it be the key to restoring his strength and revenge against The Doctor by destroying the world he treasured, but it would also be the means to becoming the God of a new universe. One where his accursed brother didn't exist, and he was free to do whatever he pleased. Mold it into true chaos and use it as a stepping stone to conquer more universes and dimensions. His brother would not be powerful enough to stop him upon his complete victory. He would end their eternal battle of good and evil.

Order and Chaos.

White and Black.

The loss of life on this planet was enough to empower him and regain much of his former strength, but he needed more. More death and chaos. The war on Earth was undoubtedly doing him great favor, and best of all, it didn't matter to him who won in the end. It powered him regardless of the means of who died in the war, be it a pony or human. His carefully conceived ritual had ensured that death itself, irrespective of the living mortal, would empower him through their entropy and dread.

The time for his ascension into his new universe was close. The Harmony Canon was a brilliant means to do so, and it made him wonder why he never chose to control Twilight Sparkle instead.

"I should thank The Doctor. His actions have made Ms. Sparkle quite the monster compared to her true self," He chuckled at the irony. Then again, it wouldn't be the first time The Doctor created his enemies. "Still, The Doctor getting caught up in Equestria's travel through dimensions was not what I had planned. And I will not underestimate him this time. He still is a danger, and I cannot let him defeat me. Not when I am so close!"

A part of him wanted to take part of his power, form himself into his servant, and take care of him personally, but so long as his true identity remained hidden, he could work through his puppet in the shadows. No, he would have others help him instead. Ones who had just as much a grudge against The Doctor as he did. He would send them with his powers. He had enough strength to do so.

Raising his hands, he used his god-like abilities to find two representatives of the evilest races in the galaxy. Ones he liked for the destruction they brought upon the universe in their growing spread of darkness. It was child's play to do so for his strength, but he had to be quick, lest his brother would find out what he was doing. Veils of the void slowly opened up, and from their iris came two figures that looked around in confusion and scanned the area.

"ALERT! ALERT! THIS UNIT HAS BEEN TELEPORTED VIA UNKNOWN ENERGY! ALERT! ALERT!"

"Where am I? What is the meaning of this? Senses indicate an unknown presence in the area and the species known as Dalek. Is this your doing, Dalek?"

"DALEKS DO NOT ANSWER TO INFERIOR CYBERPONIES! YOU WILL ANSWER MY QUESTIONS AND TELL ME WHERE I AM! OR YOU WILL BE EXTERMINATED!"

The first of the fingers was known as a Dalek. Formerly of a species known as Kaleds from the planet Skaro, they were mutated beings created by the genius and yet mad scientist, Davros. Since their ascension into space, the Daleks had built an empire of conquest and extermination in which they sought to destroy all life in the galaxy except their own. They felt no pity, no concept of mercy, and they hated everything that wasn't of their own kind with extreme prejudice.

The second was known as a Cyberpony. Initially from Equus's twin planet, Mondas, it was knocked away by a comet which made the planet highly radioactive. They replaced parts of their dying bodies with cybernetics. Eventually, they added emotional inhibitors, suppressing all feelings – love, hate, even fear. To survive, they took over words and converted any species they could into fellow Cyberponies, eliminating all others or forcing them into servitude.

They were among the most technologically advanced races in the galaxy and among the most feared. But they would do nicely for the evil he was planning.

"I was the one who summoned you," He spoke with such power that it echoed in the cave that stood as the Tree of Harmony's memorial. "I have summoned you because I have need of you."

"DALEKS DO NOT ANSWER TO ANYONE! YOU WILL ANSWER TO ME!"

The being laughed at the creature that was an ant before him. "You have no power over me, mutant. I am far older and more powerful than you could dream."

"YOU WILL NOT MOCK ME! YOU WILL BE EXTERMINATED!"

The Dalek fired the energy from its gunstick only for the beam to be harmless, ignored, and bounce away off the figure's frame as if it was merely a rubber ball. The Dalek fired several times, but the results were the same.

"It seems,"The Cyberpony muttered as it calculated what was happening and reached a quick logical conclusion. "That this being's abilities are far outside your own."

"NO! THAT IS NOT POSSIBLE! DALEKS ARE THE SUPREME RACE OF THE GALAXY! WE HAVE NO EQUAL!"

"And yet I am unphased by your pathetic attempts to attack me. Now be silent and act smart like your monotone friend here," The being hissed before turning to the Cyberpony. "Unless you wish to try your luck?"

"Negative."

"Good," He sighed and rolled his eyes. "Honestly, I didn't bring you halfway across the galaxy for nothing. Like I said, I am in need of you, and I will offer you a reward for doing so."

"And what is it that you have in need of?"The Cyberpony asked.

"Currently, I have a plan to take over a new universe that lies in a different dimension. Pieces are in place for my ascension into it where I will be unchallenged in power and rule it however I see fit."

"How did you accomplish this? Dimensional travel has only been theorized and never successfully done."

"EVEN DALEKS HAVE LIMITED SUCCESS IN THE CREATION OF ACCESSING ALTERNATE DIMENSIONS!"

"I have my ways. Needless to say, it's thanks to the Equestrians, who I am currently manipulating into a war with a race known as humanity, which is the only race in this universe. The first of its kind, you could say," He answered before leaning forward. "However, one threat stands in the way of this plan of mine. An enemy we all share and one you are very familiar with: The Doctor."

"THE DOCTOR?!"The Dalek shouted louder than ever. "THE DOCTOR IS THE ENEMY OF THE DALEKS! HE MUST BE EXTERMINATED!"

"He is also the enemy of the Cyberpony race. His elimination is highly required for our domination of the galaxy," The Cyberpony started with a little bit of anger. It amused the dark being to see that the so-called "emotionless" race could sometimes show such things when pushed.

"Yes, and I require your assistance in eliminating him, and all the remaining Equestrians and Humans should my original plan fall apart. Do this for me, and I will grant you access to the universe I seek to take over. You can even fight for it if you wish. It will amuse me."

"WHY SHOULD WE TRUST YOU?!"

"Indeed. What assurance do we have that you will not betray us?"

"Well, I could just do this to you," He said before his pure black eyes glowed, and he snapped his fingers.

In an instant dark energy erupted from the bodies of the Dalek and Cyberpony, who screamed in horror and pain as they were tortured by his power. Their mechanical bodies sparked and spewed as their cries of pain echoed. Their systems completely malfunctioned, and their brains scrambled to try and make sense of all of this, but they were too much in agony to do so. After letting them suffer for a bit longer, their abuser snapped his fingers, and the pain ended. The two gasped and wheezed as they struggled to regain control of themselves.

"Now, are you going to help me, or should I just get rid of you two and try to convince another Dalek Commander and Cyber Leader to take my deal?"

"....I OBEY."

"...As do I."

"Good. Now I will send you back, and you will gather the forces under your command to these locations that I will send to you telepathically. From there, you leave the rest to me. And you will follow my orders to the letter. Fail to follow them or even THINK of betraying me? I will make what you suffered from pale compared to what I will do to you. Understood?"

"I OBEY."

"Affirmative."

"Good. Now begone." He said as he waved his claws and sent the two back to their original places in the universe. Smirking, he whispered, "Soon, Doctor. Soon I will have my revenge."

Author's Note

Alright, guess the baddie. If you didn't get it by now, you'll have to wait for the next chapter which will be two weeks from now. I left the biggest clue here so all you Whovian fans should get it.

As always, please help out at the NegotationsVerse TV Tropes Page. We even have a Regeneration Focus section: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 11

“So, let me ask you a question about this brave new world of yours. When you've killed all the bad guys; and when it's all perfect and just and fair; and when you have finally got it exactly the way you want it, what are you going to do with the people like you?”

-The Twelfth Doctor

+}{+

"YOU WANT TO WHAT?!"

Luna winced upon hearing her sister's "Royal Canterlot Voice," especially since she was beside her. Most ponies assumed that Luna had the bigger volume considering she used it more often, but Celestia had the bigger lungs between them.
And the scarier attitude when she was angry.

It took a lot to make Celestia upset, but this war and the problems it had been causing had made the Sun Princess angrier than Luna had ever seen her. Luna couldn't blame her sister since everything had gone wrong since Osaka. They had suffered defeat after defeat with their greatest weapon, the Conversion Potion, being reduced to little more than a nuisance to humanity ever since their newest enemy, The Doctor, created a cure for it. More and more Equestrians fled like cowards to the enemy side to save their hides as the going got rough. And then there was the aftermath of the use of the Crystal Cannon.

Princess Luna was not squeamish from seeing a significant loss of life in war, but the results of the cannon had made her sick to her stomach. She didn't like humanity. They were children who acted like brats and made messes that they refused to clean up, hurting not just themselves but the planet they lived on.

She had tried to keep an open mind, but that stopped after the assassination attempt on her life when she was touring Europe during their early days of visiting the human lands. They had no honor or care for their planet and were selfish.

Yet Luna regretted saying "yes" to the Crystal Cannon.

Researching human warfare, Luna learned that the makers of the Atom Bomb regretted what they had created after the bombings of Hiroshima and Nagasaki, and Luna couldn't help but compare her feelings to this. She had been reluctant to use the weapon since it was such a dishonorable method of warfare. It was a weapon initially constructed by that tyrant, King Sombra, which lowered her view of it even more. The aftermath, however, was what really made her regret her decision. She knew it would be destructive, but not that destructive. Millions of those lives just gone like that, including some of their ponies.

Yet that isn't the worst of it, Princess Luna thought as she closed her eyes in frustration. It's further divided us as a nation.

Half of Equestria was now rebelling against them and demanding an end to the war. Entire regiments and divisions were going AWOL, with the largest being led by Corporal Valkyrie, who advocated surrender and overthrowing the whole Royal Family for their crimes against humanity, pony kind, and all other life back home. Apparently, the false rumor of them leaving their homeworld to die was spreading more and more, regardless of what they did.

The division was also among their nation's heroes. The Elements had all but ended their friendship with Twilight and made it clear they refuse to use their Elements in such a way ever again. Princess Luna may not have been an expert in friendship like Twilight was, but even she could see her bonds with her former friends being ripped apart over time by her actions. Her cold behavior, inability to talk about her issues, and the stress of her brother's death combined with the war had turned the mare that Luna thought of as one of her closest friends into a shadow of herself. It was bad enough that Applejack, Rainbow Dash, and Rarity had all ended their friendship with Twilight after Pinkie Pie's suicide, but when Spike, of all beings, abandoned her?

Luna knew things were bucked up.

The final break of their broken family came when a hysterical Cadence told them all that Flurry Heart had run away with Spike to the humans. Now Luna was fighting against her niece, which was the final straw. Flurry Heart and Spike declared themselves traitors and would side with their enemies to end the war once and for all.

"We must end the war, Sister," Princess Luna proclaimed again to Princess Celestia, who was staring at her in disbelief over the war room's map. After meeting with their remaining generals, Luna asked Princess Celestia and Twilight to stay behind in private to discuss something important.

"You want...to end the war...you want us to surrender?!" Princess Celestia shouted with fury, her right eye twitching, which made Luna even more determined to continue.

"Not surrender. Negotiate," Princess Luan corrected before sighing. "Sister, it's time to face reality. Half of the nation hates us and is rebelling. Our forces are too stretched to do anything to continue fighting the war. We're fighting our own ponies now, and I will not see Equestria further divided than she already is. We have never been this divided since before Equestria was made. If the wendigos were here, they'd be having a feast!"

"They just need to be reined in!" Princess Celestia growled as she flared out her wings. "They need to realize that our true enemy is humanity!"

"An enemy that is more united than us and refuses to back down even in the threat of annihilation," Princess Luna pointed out, and there was some admiration for that. She could find some approval for how humanity, even after all this, refused to give in and continued to fight. The warrior in her could respect that. "Sister, whatever task we hoped to accomplish in saving humanity is pointless at this point. Not when we're unable to save ourselves from our own self-destruction. We are fighting a war on two fronts, foreign and domestic, and it's clearly pointless. The war has lost favor, and our subjects are seeking us removed from our positions because we have clearly gone too far."

"You wanted this war just as much as the rest of us, Luna," Twilight muttered darkly while hiding behind her long mane. Princess Luna couldn't help but wince at how Twilight looked. Her hair was long, and a mess which hid her bloodshot eye, her hooves unpolished, and her coat was ruff and dirty. She wasn't evening wearing her royal regalia and instead just walked around with an aura of solemn anger.

"I did," Princess Luna admitted, and she would never doubt that. "I believed in the cause we had. It was a just cause for the greater good of all, both human and Equestrian. But we need to be realistic. We have a divided army and a split populace. Our economy is on the brink, resources are scarce, chaos is rampant, and humanity is united against us in their hatred. Sister, Twilight, I'm sorry, but the war is lost. We need to negotiate a ceasefire or something before it's too late."

"Negotiate? After what we did?" Princess Celestia hissed, shaking her head. "Don't be naive, Luna. After what we did with the Crystal Cannon, humanity will see us all dead. They have already launched nuclear weapons at us. We would all be dead if we didn't have the barrier."

"Perhaps, but I'd rather take a chance to save what we can than lose it all," Princess Luna sighed as she felt the weight of a nearly four-year-long war come down upon her. "Sister. We have lost good friends and family. Our own niece has left us to join humanity, regardless of how her father died, and Cadence is in such a hysterical mess of guilt and shame she cannot rule anymore. The nobles there are this close to overthrowing her and leaving Equestria, and we'll lose the magical crystals we need for our army and our way of life. If there was any other option-"

"There is," Princess Celestia muttered as she turned to Twilight. "We can use the Crystal Can-"

"NO!" Princess Luna shouted in a fury, this time with her own Royal Canterlot Voice. "I have made it clear that I will never use that weapon again! Cadence will not do so, and we agreed that all four of us needed to agree to use it at all! Besides, the Elements of Harmony refuse to use their elements again! I will not let us force them into another traumatic moment so soon after our last use! Especially since it led to Pinkie Pie killing herself from the sure guilt of it!"

She couldn't help but glare at Twilight in disgust. "And you, Twilight! I expected better of you! To even suggest that with my sister after what you lost?! Are you mad?!"

"No! I'm bucking realistic!" Twilight shouted as she showed her eyes fully beyond her mane, and Luna nearly backed away from the sheer intensity in them. "It's no longer a war about saving humanity, Luna! They are beyond saving! It was a mistake to even try! It's a war for survival! Ours or theirs! Our hatred is too far to save any friendship or peace, especially when they are willing to go so far as to eradicate us! Even if we agreed to negotiations, what do you think will happen to us?! Will we be executed or jailed for life! Our way of life would be ruined! The ponies would be leaderless! And we might as well kiss Equestria goodbye!"

"...Is this the speech of a Princess who worries about our subjects or a traumatized filly who cannot move on from her brother's death?" Luna stated harshly. She quickly summoned an energy shield to block Twilight's magical blast.

"ENOUGH!" Celestia roared despite Twilight and Luna glaring at each other hatefully. "I will not have you two come to blows! Clearly, neither of you is mature enough and willing to focus on the bigger picture of what to do for our home! We will deal with this later!"

"No, we will deal with this now!" Luna shouted as she stomped her hoof on the floor. "Celestia, I am-"

"You will take our forces and recover the southern territories at once," Celestia ordered without once glancing at Luna and instead put her hooves on the war table and glared at it. "Once you have done this, you will return home, and we will discuss what to do next."

"You want me to lead our forces against our own kind?" Luna asked in shock.

"I want you to lead our forces and establish order once more for those under our protection," Celestia repeated with gritting teeth. "If these rebels continue to waste our time and resources, then we have no choice but to use violence against them. I am no longer playing games. I am tired of dealing with children who do not understand the bigger picture at stake. Let them hate me for what I do, but I will save them, even if they are kicking and screaming. I did so once and will do it as many times as needed for the greater good!"

"...What are we fighting for, Tia?" Luna whispered as she closed her eyes and shook her head. Princess Celestia froze upon hearing her nickname from the gentle voice of her sister. "What is this war about anymore? Saving the humans? Destroying them? Protecting Equestria? Keeping our ponies safe? Ruling the world? Bringing Harmony to Chaos? Showing the light of friendship? Or is it just for our own pride?"

Lowering his head, Luna bit her lip. "Celestia, I love you. You are my sister. But I want to know what this is all for, Celestia?"

"It's for our survival," Celestia whispered, turning away. "It has always been about our survival from the very beginning. All for the greater good. It doesn't matter what happens. So long as we survive. So long as we survive, it is worth it."

Upon hearing this, Luna's breath held. Her mind went through a dozen thoughts before slowly stopping at one. One thought that she always pushed away, but now she couldn't help but wonder. Looking at her sister, seeing her state, and hearing her talk about their survival and what she has always done for the greater good made Luna think about a particular speech from a certain green-coated traitor months ago. Luna had sworn that she would always trust her sister after her exile. She would never doubt her again and always believe in the best of her.

But just this once...just this one time...she would doubt.

"Celestia," Luna muttered, trembling slightly in her hooves, "if it has always been about our survival...why did we come here in the first place and not stay at home? Were we in danger? Is there something you are not telling us?"

There was silence.

"Cele-"

"I GAVE YOU AN ORDER, LUNA! NOW GO!"

"...As you wish," Luna whispered as she bowed and slowly left the room.

And just like that. The trust was forever shattered.

+}{+

She didn’t cry.

Not until she was back in her chambers with her closest and loyal guards.

Celestia and Luna had fought before. It was expected when it came to sisters. The furthest it ever got was the night before Luna turned into Nightmare Moon and rebelled against her sister while lost in her darkness. Luna could remember that night clearly every single time she thought about it. How her soul was filled with anger, sorrow, and hatred. Hatred was at herself, her sister, and Equestria as a whole. No matter what she did or how hard she tried, Luna could never be better than Celestia. Even after returning after a thousand years, Celestia was always the better sister, and Luna accepted it.

Luna had close friends and family. She had her followers, her subjects, and those who admired her night even if they admired the day more. She had taken all of that and found the contentment in her life to find inner peace.

Now it was all falling apart.

Her home, subjects, friendships, and even her family? It was all falling apart, and she didn’t know what to do.

No, I know what to do, Luna thought as she rubbed her eyes while looking outside her balcony. I’m just afraid to do it.

“Your Majesty?” She turned around and saw one of her loyal guards before her. “What are your orders regarding your sister’s orders?”

Luna sighed and lowered her head. It all comes to this, doesn’t it? How did everything come to be like this?

She could remember the days before they arrived here on Earth. They were happy, carefree, and peaceful. Was this their punishment? For leaving their duties on their homeworld to save a world they invaded? Were they really so weak to be divided like this? Did Luna make another mistake, or was she about to make another one?

Luna was tired. Of the war, the infighting, the madness.

It had to end.

“Tell our forces we will make for the southern territories, but we will not go to war with them,” Princess Luna whispered. “We will seek to ally with them.”

Civil War.

The moment she went there to ally with them and join them to support ending the war, it would be a civil war.

Again.

Again she would be betraying her sister.

But I am not betraying Equestria. I am trying to save her, Luna thought as she looked up at the moon. You know. This moon of Earth. It’s not so bad.

But it wasn’t the one back home.

It wasn’t her moon.

And she feared she would never see her moon ever again.

+}{+

"I shouldn't have yelled at her like that," Princess Celestia whispered as she slowly brought a cool bottle of wine towards her lips. "I don't know what came over me..."

"It's just the stress," Twilight whispered as he comforted her mentor by patting her on the back with her wings. She also wasn't happy with how she snapped at Luna, but a part of her wasn't because of what Luna said involving her brother. "She'll come around eventually."

"We don't have time," Princess Celestia groaned as she rubbed her head. Her nightmares were getting worse. It was like an omnibus doom was approaching and needed to be stopped before it was too late. "Much as I hate the concept of using the cannon despite the problems it has caused so far, you are right, Twilight. We have no choice. The humans cannot be saved. They must be destroyed until they are too weak to fight or there are not enough to mount a resistance."

"So we will use the Harmony Cannon again?" Twilight asked. "Even without Cadence and Luna's say in it."

Rubbing her forehead to ignore the strange whisper in her mind, no doubt from a lack of sleep, she nodded. "I'll take full responsibility for their anger. However, we must be sure to not target Geneva. I still want to save Flurry Heart and Spike. I want them to come back to us."

"Understood, we'll pick somewhere in Asia this time. I believe Japan will be a good target, along with the other Asian nations around it like the two Koreas, China, and some of Indonesia," Twilight suggested.

Princess Celestia didn't need to be a mind reader to know that Twilight wanted to mainly use it for revenge against Japan for her brother's death, but it didn't matter in the end. So long as it wasn't where Flurry Heart and Spike were, she didn't care. "Yes. That will suffice."

"We still need to convince my friends to give up their Elements, or should we go with the alternative idea?" Twilight asked curiously.

"... I'll make the order, but are you sure? They may never forgive you for this."

"Like you said before," Twilight sighed deeply. "Let them hate me for what I do, but I will save them nonetheless, even if they are kicking and screaming."

+}{+

Celestia, I hate hangovers. Rainbow Dash moaned and rubbed her head. Why didn’t I stop after six? I always need to go beyond.

Rainbow Dash kept her eyes closed as she let the throbbing in her head continue to pound her skull. She could feel a cold metal surface on her back and wondered where she ended up blacking out this time. Hopefully, it wasn’t as bad as when Dash woke up chained in an S&M club in Las Pegasus with Fluttershy when they went out to celebrate her twenty-first birthday. It had been really embarrassing trying to get out of that black latex suit, and she was sure Fluttershy would have a panic attack upon finding out she got a tattoo on her flank that read “Spank Master” with a heart on the cheek.

Chuckling, Rainbow Dash remembered how Fluttershy swore to never drink again after that day and to never have it brought up again. However, her chuckles soon turned to soft sighs. Fluttershy...

Rainbow Dash missed her.

She always missed her.

Whenever Dash told ponies who mentioned Fluttershy that the pegasus was dead to her, the speedster would always feel her heart crushed upon muttering those words. Whenever Rainbow Dash flew near Fluttershy’s burned cottage, she sometimes paused and imagined the yellow feathered mare working on her garden nearby. It never was the same after Fluttershy defected. Everything just fell apart when she left.

The six of them were supposed to be sisters forever, yet one friend had abandoned them, one killed herself, and the other? Buck, I don’t even want to think about Twilight. Not right now.
Rainbow Dash sometimes wondered if she ever took her friendship with others for granted, especially Fluttershy. They never laughed at her dreams, always trusted her, and supported her every single step of the way to help her at the worst of times. They were more than friends to Rainbow. They were her family.

And some family we turned out to be, Dash bitterly thought as she slowly got up but kept her eyes closed while rubbing her head. I should talk to Applejack or Rarity. I haven’t...I haven’t since the funeral. Maybe we can save whatever is left between the three of us and figure out what to do next.

“R-Rainbow?”

Dash’s eyes opened wide upon hearing Rarity’s voice nearby. However, her curiosity about why she was hearing her fashion-loving friend was soon forgotten upon seeing that she was in a stone room with nothing but a bed and toilet seat. Yelping, Rainbow Dash flipped out of the bed she was on and tried to fly out but hit her head on the ceiling, making her headache twice as bad. Moaning, she floated down and rubbed her forehead before glancing forward. Instead of a cell door, like she had been expecting, there was a magical green forcefield, and she pressed her hooves against it only to find it completely solid. Each attempt to kick it down only caused small ripples of energy to spread on the shield. Frustrated, Rainbow Dash kicked it again before shouting, “What’s the big idea?! Who’s behind this!”

“Rainbow!”

Remembering that she wasn’t alone, Rainbow Dash looked across the hallway of the black crystal dungeon she was in and saw Rarity in a similar cell across from her. “Rarity? You too?”
“Yes, I’ve been awake for an hour, I think. Waiting for you and Applejack to get up,” She answered with a huff.

“AJ is here too?!” Rainbow Dash shouted.

“Not so loud! Mah ears are still ringin’!” Based on the direction of the farmer friend’s tone, Applejack appeared in the cell next to her on the right. “Alright, who in tarnation kidnapped us this time, and whose flank Ah gotta kick?”

“Was it the humans or the Underground Railroad?” Rainbow Dash asked, looking around for any clues as to who their current jailors were.

“First off, I think you can write off the humans since they don’t have access to magically shielded cells,” Rarity pointed out, rolling her eyes. “And second, you don’t need to bother guessing because I already know who took us. It was the ESS.

“The ESS?!” Both Applejack and Rainbow Dash shouted in confusion and surprise.

“Why would they kidnap us?!” Rainbow Dash shouted in disbelief. “We’re the Elements of Harmony!”

“I don’t know, but I remember seeing one in my kitchen when I went to get a glass of water. I remember calling Valiant Wave for help, but he hit me with a spell, and then I got really tired before blacking out. Next thing I know, I woke up here,” Rarity explained while looking worried. “I haven’t seen him either. I hope he’s okay...”

“Ah think Ah heard somepony in mah room at night, but Ah felt so tired. Ah just went back to sleep,” Applejack said while yawning.

“I guess we both got hit with a sleep spell,” Rarity theorized before turning to Rainbow Dash. “Dash? What about you?”

“Uhhh, Spitfire and Soarin wanted to go drinking, and I know I took in many shots before...um, blacking out?” Rainbow Dash answered with a nervous chuckle.

“Wow, either they knocked you out by slippin’ somethin’ into yer drink, or ya did the work for them, and all they needed to do was drag yer sorry drunken butt here,” Applejack chuckled.

“Laugh it up, AJ. Laugh it up,” Dash grumbled before shaking her head. “Okay, so we all got targeted by the ESS, but does anypony know why?”

“Because Princess Twilight ordered us to do it.”

There was a sudden drop of silence so swift that Rainbow Dash could feel her heartbeat in her chest like a drum solo. Turning to the right, she watched a familiar pony from Ponyville walk over to them wearing a black trenchcoat and a crystal wrist shooter on her right leg. “B-Bon Bon?”

“That’s Agent Sweetie Drops,” Their fellow Ponyville resident answered with such a cold glance that Rainbow Dash felt her spine shiver.

“You’re a member of the ESS?” Rarity asked in disbelief. “You have to be kidding me! You’re a candy maker!”

“Former member of a monster hunting agency operating in Canterlot, actually. I retired after a mission with a Bugbear went wrong and laid low in Ponyville under a new name,” Agent Sweetie Drops sighed as she shook her head. “I tried to have a normal life, but after everything that happened with the war, I couldn’t stand by and let Equestria suffer under the hands of traitors and doubters. So I joined the ESS and became one of its agents.”

“And Lyra never suspected?” Applejack asked.

“That mare never did. I tried to forget about my past and focus on being the new me. My biggest mistake was not focusing enough on trying to stop Lyra when she started sympathizing with those monkeys. I should have snapped her neck the moment I learned she was going to go so far with her betrayal as she did,” Agent Sweetie Drops growled as she spat on the floor. “But enough about her. She’s not important. You need to understand that you are here because Princess Twilight and Princess Celestia have ordered you locked up.”

“What?! What for?!” Rainbow Dash asked.

“To use our Elements for the Harmony Cannon, right?” Applejack spat in disgust. “Figures. Twilight never could take no for an answer. Even from her friends.”

Rainbow Dash almost shouted that Twilight wouldn’t do that before stopping herself. No...I can believe it... I just don’t want to believe it.

Twilight was not the Twilight she knew, and Rainbow Dash knew it. She knew the alicorn was obsessed with destroying the Doctor and winning the war since Osaka. But there was always some hope in Rainbow Dash that a part of her old friend was still there, and she wouldn’t go this far. But here I am, a prisoner on orders by my so-called “friend” and the Princess I gave everything for. Buck damn it.

“What did you do with my Valiant?!” Rarity demanded, huffing her nose.

“Your lover managed to get away, but it doesn’t matter. He’ll be hunted down soon enough and silenced,” Agent Sweetie Drops said, which made Rarity gasp in horror.

“You would kill an innocent pony just like that?! Why?!” Rainbow Dash shouted in disgust.

“The mission required that nopony knew we kidnapped you. When it comes to missions like these, you need to tie up loose ends,” Agent Sweetie Drops said with a shrug.

“He’s not a loose end! He’s the stallion I love!” Rarity screamed with tears in her eyes. “You so much as touch a single hair on his chest, and I’ll bucking kill you!”

Agent Sweetie Drops ignored Rarity and walked forward until she was in front of all three of them. “Listen, Princess Twilight and Princess Celestia will be here to explain everything to you in person. All you have to do is behave and listen to them. We have orders to keep you safe and protected, but we aren’t spoiling you. So you’ll be fine if you don’t cause trouble.”

“Bon Bon, listen to me!” Rainbow Dash shouted while pressing herself against the shield of her cell. “Twilight and Princess Celestia want to use our Elements to fire the Harmony Cannon and kill millions more humans! You can’t allow this to happen!”

“I thought you were a soldier, Dash?” Agent Sweetie Drops snorted. “Why do you care about a bunch of humans?”

“BECAUSE WE WERE WRONG!”

Rainbow Dash didn’t even know she had said it until it came out of her mouth. Everypony stared at her as she finally said it. The one thing Rainbow had been dreading to admit deep down but had no choice but to finally face the music. She fell to her hunches and bitterly began to weep.

“We were wrong. Lyra was right. We’re the bad guys. We’re the Nightmare Moon, Chrysalis, and Tirek in all this. We screwed up, and we started a war of genocide. I didn’t see it until the Harmony Cannon; I don’t want to admit it, but I have to. Pinkie Pie saw the truth and couldn’t live with the guilt. Spike and Flurry Heart always saw the truth but stayed silent until they finally took action. Fluttershy and Discord took a stand when it was needed, and they’re acting like real heroes. Me? I can’t deny it anymore. I just can’t!

Rubbing her teary eyes, Rainbow Dash looked at Sweetie Drops eye to eye. “I don’t want to keep fighting anymore. I want this to stop. I want to go home. I want to go back! Back when we were real heroes! Back when I wasn’t a murderer! Back when we were the actual good guys instead of the monsters that I keep looking into the mirror every day! I want to...”

Taking a deep breath, Rainbow Dash muttered, “I want to be worthy of Loyalty again.”

“...Me too,” Rarity whispered as she lowered her head in shame. “I want to be Generosity instead of Genocide again.”

“...Buck it, me three,” Applejack sighed and shook her head. “Ah don’t like humans, but Ah can finally understand what we did was wrong to them. Too late, mind ya, but better than never, Ah guess.”

Agent Sweetie Drops glared at all three of them one by one. “So you all share these treasonous thoughts?”

“Oh, buck...you know what? I’ll use the human term,” Rainbow Dash growled. “Fuck off, Agent Kiss-My-Flanks Drophead! If finally doing the right thing means being called a traitor, then get the fucking rope and hang me right now! Because fuck you! Fuck Celestia! AND FUCK TWILIGHT SPARKLE!”

Rainbow Dash took a few more deep breaths before shaking her head. “Tell Twilight and Celestia I’ll die before I use my Element again. I’m done.”

“Me too,” Rarity said.

“Ditto,” AJ calmly agreed.

Agent Sweetie Drops just huffed and shook her head. “You disappoint me, girls. You disappoint Equestria.”

“This is not Equestria,” Applejack whispered, shaking her head. “This is not the Equestria we grew up in. This is Hell.”

Agent Sweetie Drops said nothing. She walked away, and the girls heard a door close behind her.

“So now what?” Rainbow Dash asked, leaning against the shield. Her little spiel against the prick of a mare felt nice, but they were still trapped.

“Ah guess we hope somepony rescues us,” Applejack suggests.

“And who is that going to be?” Rarity asked.

“Ah don’t know. But at this point? Ah take anyone.”

+}{+

Deep below the basement of Fort Obsidian, a blue box slowly came into materialization and landed safely behind a series of old crates that hadn’t been opened in years. The doors opened and The Doctor poked his head to make sure that things were in the clear. Taking out his Sonic Screwdriver, he activated it and scanned around before nodding and walked out. Following him were his companions and Spike who all stood before him ready to take part in their most important mission yet.

“Everyone knows their objectives?” The Doctor asked as they all nodded in agreement. “Good. Now then. Tally-Ho.”

Author's Note

I like writing the side of the ponies on the losing side. This part wasn't supposed to go this long but it ended up going longer then I thought. Next time, The Doctor strikes again.

Please Help Out at the NeogtationsVerse TV Tropes Page: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 12

“What’s the point in two hearts if you can’t be a bit forgiving now and then?”

-The Eleventh Doctor

+}{+

Corporal Diamond Watch didn't know what to feel about his position at Fort Obsidian. As a Crystal Pony who grew up during the reign of Sombra, the thousand years in suspended animation exile, and witnessed the destruction of the monster once and for all, he had hoped to never again have to deal with anything associated with the tyrant ever again.

Yet, here he was as a member of security for not only one of the former king's top hidden fortresses but also part of a project based on one of his worst weapon designs. Which was approved of by the princesses he had pledged his loyalty to, but it was getting to the point where the pledge felt like ashes in his mouth.

Diamond Watch didn't particularly have an opinion on the war. He had read about some of the worst humans in history before such books became outlawed. A number of them made King Sombra look like a puppy in comparison, and he agreed, to an extent, that the humans were a threat to ponykind.

Somewhere down the line, a human with great power would try to rule or exterminate them, and if they could prevent that, Diamond was all for it. However, as the war continued, more extreme measures were being taken to achieve victory. Measures that reminded him of the dark days during the reign of his former king. Diamond couldn't help but wonder if he was destined to constantly live under the throne of some tyrant one way or another.

The ban on certain goods, silencing foreign viewpoints and opinions, arresting those who spoke out against the crown, the war, the jailing of non-ponies, the ESS, and the Harmony Cannon.

If there was an afterlife, King Sombra must have laughed at the irony of what had become of them after his death.

He was not blind, like the non-Crystal Ponies, about what a tyrant was like, and the Princesses of Equestria were becoming more and more like that every day.

Diamond Watch sighed as he looked at the crystal screens from the "Beholder Eyes." The Beholder Eyes were based on the now-extinct demons who could cast dangerous spells with their eyes to the point that gazing upon them could kill you with fear instantly.

Thankfully, these devices were just stone eye-like objects that could move left to right with a giant crystal that could capture the visualization of everything in front of it with sight-based magic and feed that image back to the crystalized screens in front of him and his partner. Say what you will about Sombra, but he was a genius when inventing security.

Said partner was a female unicorn pony from Canterlot who, sadly, supported everything going on. Naturally, Diamond had to pretend to be one because, deep down, he was a coward. After all, if he didn't speak up against Sombra, how would he speak out against Princess Celestia?

"So where do you think the Princesses will target the Harmony Cannon next?" Long Lilly, pink mane flowing past her right eye, asked as he sighed and gazed at her. "Personally, I'm hoping for Amsterdam. I lost a good friend in that battle, and I've been hoping for a chance to go back and raze it more to the ground than we did."

"I don't know. Does it even matter? Even after the first use of it, the humans refused to surrender or do anything," Diamond Watch pointed out.

"Hey, if they want to all die in futility, I'm not going to cry tears for them," Lone Lilly snorted.
Before Diamond could say anything, there was a knock on the door.

"Muffin Delivery!"

This made the two guards pause and tilt their heads at each other.

"I didn't order muffins. Did you?"

"No, but we'll see what this is about."

Diamond Watch got up from his seat and walked over to the door. He pressed the button to open, only to see a purple hoof come right for his face and knock him off his hooves to the ground, where he was stone-cold knocked out. Lone Lilly got up in shock and readied her horn, but Dinky was faster and hit her with a powerful blast of magic that also knocked her back and sent her into unconsciousness.

Lyra and Carrot Top were already getting the bodies and placing them into the nearby closet as The Doctor, Derpy, Fluttershy, and Flash Sentry walked over to the screens the two guards were previously looking at.

"Muffin delivery? Really?" Flash Sentry asked with a deadpan expression.

"What? It worked, right?" Derpy pointed out with a smile.

"I'm still surprised the TARDIS didn't get picked up by the Beholder Eyes," Fluttershy said with surprise as she looked at the crystal screen where they had landed in the blue box, only to not see it there.

"Yes, well, after getting constantly watched on by UNIT, Torchwood, and so many other agencies in the past, I finally put in a little gizmo that lets the TARDIS get ignored in any sort of visualized medium including those around it in a thirty feet radius," The Doctor said as he took his Sonic Screwdriver and started waving it around the crystal screens. After a few seconds, they all went static before returning to their proper settings. Looking at the glowing end, The Doctor nodded. "Excellent. I have control of all the Beholder Eyes."

"So where is the Harmony Canon?" Lyra asked, looking at them intently.

"It should still be in the same place that Twilight showed it to us last time," Spike said with a growl. Sure enough, the Doctor made it appear on one of the screens. Naturally, there were a lot of guards and scientists working around it.

"Look at the size of that thing," Carrot Top whispered in awe. "Are you sure this plan is going to work, Doctor?"

"Please, I've taken down bigger weapons of mass destruction than this," The Doctor scoffed as he changed a few screens with his screwdriver, and various rooms appeared until he found what he was looking for. One was a potion lab filled with elixirs and ingredients, and the other was what appeared to be a storage for various magical crystals from the Empire in multiple quantities.

"Alright, found what we are looking for," The Doctor said as he turned to the group. "For this sabotage to work, we will need the chemicals and crystals I told you about. You have the notes?"

Lyra and Flash Sentry nodded and showed their lists from their saddle bags.

"Alright, then, we stick with the plan. Discord's diversion is going to occur soon. I'll be here monitoring everypony and giving instructions. You all have your communicators?" The group all pointed to their ears where electronic ear pieces were placed, modified for their ear shapes, with small mikes that could be used for communication. "Excellent. Then our first group shall consist of."

"Applejack, Rainbow Dash, and Rarity?!" Spike shouted in surprise, which made everyone stare at him.

"Um, I don't think the former Elements of Harmony are in our group, Spike," Dinky pointed out but soon turned to where Spike was staring and gasped. "What the hay?!"

The entire group stared as one of the screens showed the prison section containing the said three Elements of Harmony as prisoners. Rainbow Dash was doing push-ups with fury on her face while Rarity was sitting on her bed, looking almost in tears, as Applejack was staring up at the ceiling while lying on her bed.

"What are they doing there?" Fluttershy asked with worry.

"...Whatever it is, I doubt it's good," The Doctor said with a sigh. "Alright, side plan. We also have to save them."

"What?!" Lyra shouted in disbelief. "Are you kidding me?! No offense, Doctor, but why should we save them after everything they've done?!"

"And what have they done, Lyra?" The Doctor asked calmly.

"They teleported us from our world and doomed our home-"

"Celestia tricked everypony into doing that. If they are to blame for being allowed for that to happen, Fluttershy should also be condemned," The Doctor said, making the shy pegasus wince and hide behind her mane.

"They supported the war. Isn't that bad enough?" Dinky asked as she also looked furious about the idea of saving them.

"So did Big Macintosh, but we changed his mind, didn't we?" The Doctor said as he shook his head. "Many who supported the war are now against it because they've finally had their eyes opened. Princess Celestia created an entire cult of personality. She has manipulated everypony into living in a world of fear of anything outside of Equestrian culture because she is afraid of being unable to control things she cannot understand or order around.

Yes, they supported the war, but how much was based on lies and manipulation rather than thinking for themselves? Sometimes the villains need to see how they are villains in the first place to earn their redemption."

"They let their Elements be used for the Harmony Cannon," Flash Sentry said with a snarl. "Millions are dead because of them. They have blood on their hooves."

"So do I," The Doctor said coldly, making the others stare at him. "Do you really think I am a saint? For every world that praises me, some curse me. Most live in fear of me because of what I am capable of. Believe me, if I really, really, really wanted to, I could destroy the entire nation of Equestria or even this entire planet in several ways. I have burned empires, destroyed planets, ended the existence of numerous aliens, and been in wars that make this pale in comparison. One that nearly ended the existence of all reality and time itself.

I have so many sins that I'll never be able to wash my hands clean of them, but I still do it not for redemption but to make sure nobody else has to go through what I do to make the galaxy safe. I will seek to end things with as little loss as possible. Always. But if the chips are down, and mercy is not an option, then you best hope the damage is as minimal as possible."

Nopony said a word. And honestly, they couldn't.

A few of them even stepped back in shock. They saw the Doctor as a paragon of virtue for so long, but if what he was saying was true. It only made them more confused. This stallion had done so much good in his efforts to save the lives of so many, both human, pony, and others. And yet, he here was confessing to having done more genocide than even the worst of humanity and Equestria's monsters.

"So why save them?" Derpy whispered, not out of anger but curiosity.

"...Because it's the kind thing to do," Fluttershy said with a heavy sigh as everypony looked at her. She gave a sad smile to the others. "I...I want to save them. I know they've done so many horrible things. I know they've made mistakes...but... they're my friends. Even if they curse, hate, or look at me with shame, deep down, I still love them. And even if I didn't, I'd still do it. Because it's the right thing to do."

"But..."

"Look at them," The Doctor said as he pointed to them. "Do those faces look like the expression of heartless monsters? No, I see regret, sorrow, and shame. I see three mares who feel hopeless and lost. Awakened from their darkness and searching for light.

I'm not saying forgive them for what they have done. It takes more than regret to make things right again; it can be a starting point. One where they can start making that path to do the right thing again.

They were once good ponies. Heroes and saviors. They had been decent folk who would do anything to help others and were lost in darkness by the actions of a mare who twisted them. They're not just asking someone to help free them from their prisons. They are also asking for someone to help them free them from themselves. From the monsters they became. And I can't ignore anyone who needs that kind of help...

...Can you?"

Everypony stared at each other before Derpy smiled brightly and stepped forward. "Okay! Let's do it!"

"Wait, seriously, Mom?" Dinky asked in surprise.

"Yup! I trust the Doctor and Fluttershy! So let's do it!" Derpy said with a big smile to her daughter.

Dinky was quiet at first before shaking her head. "Sometimes, Mom, you are too nice for your own good. But that's what makes you the mother I love and respect. I'm in."

"...I guess we might as well," Lyra sighed heavily. "I don't like it, but I get it. Equestria was once about helping others when they needed it the most. We can't let them rot in prison as victims of Celestia's madness, even if they were once a part of it."

"Plus, it would deny the Princesses the other Elements, and if we get them to turn traitor, it will only look bad for them," Flash Sentry said with a shrug.

"...They're my friends too," Spike answered as he gripped his hand. "Those girls... they're my sisters in all but blood. We've been through too much for me to completely abandon them. If they really are sorry for what they've done... if they are the girls I grew to love for all those years, then we have to rescue them."

Carrot Top sighed. "For the record, I think this is a bad idea. But I guess I'll trust you, Doc."
Fluttershy's eyes turned to steel, and she nodded. "Let's do it."

"Right! Here's the plan!" The Doctor said as he gathered them around.

+}{+

When Fort Obsidian was refurbished to suit the needs of Princess Twilight’s project of the Harmony Cannon, she wanted to guarantee that it had all the necessary protections.

To that end, she ensured that there were multiple watch stations around the fort. There were three rings of watch towers starting from three miles, seven miles, and ten miles. All were given top-of-the-line radio equipment to report any disturbance or attack that would alert all the other watch towers, the main base, and The Crystal Empire so that reinforcements could be sent.

Since they were formed, none of them had since reported anything suspicious or dangerous. However, today would be the day when all Hell broke loose. One of the far outer ring watch stations was huddling up and trying to stay warm as the winter weather was colder and more furious than usual.

Most of the group gathered for lunch save for one lone Earth Pony who was keeping watch in their station’s tower while wrapped in three blankets with frost on them. Shivering, he kept still a lookout at the snow field in the distance of nothing, only to notice that a large storm cloud was forming and heading straight for them.

At first, he grumbled at the prospect of it suddenly getting colder to the point that he was thinking of getting two more blankets, only to pause upon noticing a storm on the horizon in the distance.

Having been born into a half-pegasus and half-earth pony family living in Cloudsdale, he had known much about weather growing up. Curious, he grabbed his telescope and lifted it to his eyes only to see the storm approaching. The clouds looked a lot lower than usual. Clouds were not supposed to be that low, even during a snowstorm. Far closer than any typical storm could commonly do so. There was also an extensive line of wispy figures in front of it. Almost ghost-like.

Something inside his gut told him that this was not an ordinary storm at all, and as it got closer and closer, the figures leading it became more apparent. When he saw what they were with a clear eye, he felt the telescope drop out of his hooves in utter shock. What he was seeing was impossible. It had to be. They were extinct. They all died a thousand or so years ago. Even if they weren’t all dead, they couldn’t possibly be here on this planet.

Yet, upon grabbing his telescope and seeing them coming so close that they were now just a few feet away, he couldn’t deny it anymore. He rushed to the emergency radio and began screaming in it just as the first flurry of ice and snow began to freeze the borders of the station, and chaos erupted from it.

Along with the shilling spectral shrieks of a long-time enemy of ponykind...

+}{+

"Absolutely not!" Cadence screamed as she threw her goblet of wine against the wall with her magic.

When she heard that Princess Celestia and Twilight were coming over, Cadence didn't even bother preparing herself for their visit. She didn't care much about anything since her daughter fled to the humans. That even extended to her fellow Princesses to the point where she barely wanted to deal with them.

They would like to talk about the war, but as far as Cadence was concerned, it was nothing compared to finding her daughter and bringing her home. She let them come into her home only because she had to play politely with them both, but now Cadence wished she tossed them out and let them land on their flanks.

"Cadence, please," Princess Celestia tried to speak, but Cadence glared at her and interrupted with bitterness in her tone.

"Don't Cadence me, Celestia! You actually want to use the Harmony Cannon again after what it did last time?! Especially since my daughter is now in the human lands and could potentially be killed by it?! Are you bucking insane?!" Cadence screamed with fury.

"Cadence, we aren't going to hurt Flurry Heart! We're not planning to target Geneva!" Celestia said in surprise.

"And what's to stop some grieving humans from taking their revenge on her? Even if Flurry Heart is a child, I cannot risk her life being in danger by our actions!" Cadence argued before grumbling. "Where do you plan on firing it anyway?"

"We're going to aim for Japan, where Shining Armor was killed, along with any other Asian nations like Korea, China, Mongolia, Vietnam, and so forth," Celestia explained. "They have some of the highest concentrations of populated masses. If we can use the Harmony Cannon there, then maybe-"

"Oh, don't you dare bring my husband into this! Let alone convince me that committing more mass murder will solve this stupid war! A war that has cost us everything because of your stupid pride!" Cadence yelled in disgust.

"Mi Amore Cadenza!" Celestia shouted sternly. "You are a princess of Equestria and my adopted niece! You are not supposed to act like this!"

"Do you really think I care anymore about what you think?" Cadence muttered as she shook her head and looked out the window of her room. "Celestia. We've been fighting this war for four years. I believed in it and thought we were doing the right thing. But ever since losing Shining... Ever since we used the Harmony Cannon... seeing so many of my own subjects turn against me, and everypony in Equestria so divided that we're on the cusp of civil war... The war against the humans seems so... pointless."

"It's not pointless, Cadence," Twilight stated as she softly walked over to her sister-in-law and put a wing around her back. "It's for our survival. The humans will never let us live in peace after everything that's happened. Even if they don't destroy Equestria, they will not see any of us alicorns live. Everything we treasure is at risk of being lost because, ever since Osaka, we have been losing this war. We only have two options left to win. Either we destroy them so much they give up and surrender, or we annihilate them all. The only thing that matters is our survival."

"So instead of saving them all like we originally intended, we're now killing them all," Cadence snorted as she glared at Twilight. "What makes us different from all the so-called villains we used to defeat, Twilight? Because I hear from my subjects that I have become just as bad or worse than King Sombra himself. And I can't help but think they are right after what we've done."

"Cadence, they are just-"

"My daughter has left because of what we have done," Cadence sobbed. She covered her eyes with her hooves in shame while weeping. "I'm such a horrible mother. I was so occupied with Shining's death that I didn't see how much pain she was in. I knew she hated the war and the use of the Harmony Cannon, but I still ignored her feelings. She left me because she believes we're in the wrong, and I know Flurry Heart. She would never have done this unless she was sure, especially since humanity killed her father."

Wiping the tears from her eyes, Cadence glared at the two. "How can I continue this war knowing that I will have to fight my own daughter?"

"Cadence-" Twilight tried to say something, but Cadence lifted her hoof and shook her head.

"No, Twilight. I love you. You are my sister in all but blood. And you, Auntie Celestia, are like a second mother to me, but I have to finally listen to my own heart instead of listening to you two for the sake of my daughter and my kingdom," Cadence muttered as she took a deep breath and stood tall. "I will do what I should have done long ago and listen to my subjects. As of this moment, I decree that the Crystal Empire will no longer have any part in the war against humanity, and we will seek a ceasefire if not a peaceful means of negotiations going forward."

There were surprised looks on both Celestia and Twilight as they stared at Cadence, who glared at them with such defiance that it made them wince. Both were struggling to come to the concept of what their fellow Princess just said.

After a long moment of silence, Princess Celestia just sighed and closed her eyes. "Cadence, we can't fight this war without the Crystal Empire. Half of our means of making war and living are due to the magical crystals your nation provides. Your subjects need our food and resources as well. If you do this-"

"We'll survive," Princess Cadence stated firmly. "The Crystal Empire will find a way to survive, but it will not do so by continuing to fight a war we have no hope of winning."

Twilight snarled and snapped at Cadence. "So that's it?! You want to give up?! Just like that?! Don't you see that we must stay together to win, Cadence?! Are you really going to let me and Princess Celestia, your family, fight this war on our own?! Let The Doctor win?! My brother's death go unavenged?! My friends have left me, Spike left me, Flash left me, and now you?! IS EVERYPONY I LOVE GOING TO KEEP BETRAYING ME?!"

Cadence just stared at Twilight and shook her head. "Twilight, the war is over. We lost. Even if you were to kill every human in the world, we would still lose because we would lose ourselves. We're no longer the harmonious ponies I once was proud to call myself as one. What we are...I don't even know, but the past me would have looked at us and seen us no different from Chrysalis and her changelings."

She then towered over a glaring Twilight and gritted her teeth. "And don't you bucking dare bring Shining Armor into this, Twilight. He's dead. Nothing you do will bring him back, and it's time we both recognized that. Shining died because of The Doctor and humanity, but in the end, we started this war, and he wouldn't be dead if we didn't do so in the first place. I don't know if we could have lived with humanity in peace, but at least we wouldn't be trying to obliterate each other out of pure hatred."

Then she pointed at Twilight. "And as for everypony betraying you? Who betrayed who, Twilight? Flash betrayed you because he stuck to his principles. Something we all forgot.

Your friends left you because you refused to take their feelings into account of what happened with the Harmony Cannon and Pinkie's death. And I overheard what you said to Spike in your argument. Quite frankly, I am ashamed of you for that one. You can hate me all you want, Twilight, but at the end of the day, I cannot do this anymore.

Call me a traitor.

Call me a coward.

Even refuse to call me a sister ever again. But I am done. I want an end to this war and my daughter to be safe and sound. Even if I must surrender my position or face humanity in whatever trial they want out of me, I don't care. So long as my daughter is safe and sound and my subjects have a future outside of war, I'll live with that."

"...You would really rather see Equestria fall than help us?" Twilight whispered with bitterness and spite.

"Equestria has already fallen, Twilight," Cadence whispered as she turned around to face the window of her kingdom. "If you cannot see it? Then I sadly have only one thing left to say to you.

She took a deep breath, turned to her sister-in-law, and said, "You have a lot to think about."

Twilight's eyes widened upon hearing this, and she began to shake. Her one good eye began to twitch, and flames began to emit from her mane. Twilight's horn started glowing with magic as Cadence bit her lip and slowly prepared herself for a fight until Princess Celestia spoke.

"Enough." The young alicorns stopped but continued to gaze at each other as Celestia stood between them. "If this is what you want, Cadence, then so be it. But as of this moment, you and the rest of the Crystal Empire are no longer recognized as part of the greater whole of Equestria. You are on your own as you wish, but I hope you know I am disappointed in you."

"Funny," Cadence growled. "I feel the same way with you both. Now get out of my kingdom."

Before any of the three could say anything else, the door was slammed open as a pale-faced and gasping Crystal Guard rushed inside as all three alicorns stared at him. He quickly straightened up and saluted, "Your majesties! Message from Fort Obsidian! It's under attack!"

"What?!" Twilight shouted with worry and rage. Wings flaring out, she demanded, "Who is it?! Humanity?! The Underground Railroad?! The Doctor?!"

"It's... It's..."

"Well?!"

“Wendigos! The Wendigos have returned!”

Author's Note

A lot of those who never changed sides before seem to be now huh? It's interesting to write.

Special thanks to zelkova48 for helping me edit this.

Please Help Out at the NeogtationsVerse TV Tropes Page: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 13

“We’re capable of the most incredible change. We can evolve while still staying true to who we are. We can honor who we’ve been and choose who we want to be next. Now’s your chance.”

-The Thirteenth Doctor

“You may disguise your features but you can never disguise your intent.”

-The Fifth Doctor

+}{+

The knowledge that the Wendigos had returned had nearly sent the palace into a panic until Princess Celestia and Cadence called for order.

Even though Cadence had all but officially declared secession from Equestria, even she knew that she needed Twilight and Celestia’s help in dealing with Equestria’s oldest enemies. They were just as much a threat to her subjects as they were to theirs, and so a truce was called between their arguments to focus on dealing with the wind demons.

Everypony thought the Wendios died out long ago since nopony had seen them since the Foundation of Equestria. There were rumors that they never really died, only hiding away and waiting for the right time to strike again.

Well, they couldn’t have picked a better time.

Equestria had never been more divided than it was now, and the Fires of Friendship that had driven them back would not save them this time. Not when so many ponies hated each other and blamed each other for either being traitors or zealots in a war already tearing them apart. And with the Elements of Harmony either turncoat, dead, or divided, they couldn’t use them to help protect them from the Wendigos. The Crystal Heart would do its job, but Cadence wouldn’t take any chances.

The three alicorns were all armored up, and Cadence ordered the army to prepare for defense while a division followed her to see the Wendigos firsthoof to assess their actions. Civilians were to be put into bunkers, and the emergency heating generator crystals were to stand by if their icy cold weather passed the shielding. Canterlot was already being warned, but Cadence practically had to force Celestia to issue a warning to all ponies regardless of their loyalty.

Teleporting to the third line of defense and observation for Fort Obsidian as they could, Cadence winced as the blistering wind and snow nearly flooded her vision. The shrieking cries of spirits were everywhere, she looked up to see the ghastly horses flying around. “Damn, they really have returned.”

“We cannot let them go further than this! Everypony, prepare for battle! Use fire spells and heat crystals to give fire elements to your weapons! Let us go!” Princess Celestia ordered as she lit up her horn and unleashed a massive burst of sunlight from her horn. The Wendigos shrieked, but it seemed to do little to stop them save for scattering them.

Archers aimed their arrows and lit them with their magic before firing them at the spirits. They went through the astral creatures, who only responded by blowing them with more wind and cold.

Cadence crafted a shield around her as Twilight replied with a powerful tornado that sucked up the current and blew it back at them. The spirits temporarily disappeared before reappearing and started scattering around, causing a thick misty hail.

Summoning her two blades, Cadence charged at one and tried slicing it, but it went right through them as well as her body which made her shiver at the touch. “Damn it, how are we supposed to fight ghosts?!”

“Just keep them distracted! We’ll think of something!” Twilight shouted by her side as she unleashed fire spell after fire spell. Celestia was already shining like a miniature sun and unleashing waves of solar energy at the creatures who would disappear before reappearing again.

“Hope you think of something fast, Twilight, or we’ll be popsicles out here!”

+}{+

Lyra had to admit, getting the crystals and chemicals The Doctor needed was a lot easier now that most of the guards were called out of the fort to deal with the situation outside.

Once the call went out for most of the guards to head out and assist with the defenses, it was just a matter of dressing up as staff members and walking around with their heads down. Thankfully, a lot of the staff was hiding or running around panicking so they could roam around without being noticed too much.

Derpy said she would find the chemicals leaving Lyra and Carrot Top to get the crystals. Their room was almost like an ammo supply deposit with numerous crystals labeled, stored, and sealed in proper containers with a number counter for how many. Some ranged from tiny crystals the size of thumbtacks to ones the size of Princess Celestia.

There were six that The Doctor required, and all of them were about the size of a full-grown unicorn horn. Carrot Top found a large empty box that Lyra levitated with her horn and started to carry it around as they searched the containers for the right crystals based on the list The Doctor gave them.

"So, what are you going to do after this?" Carrot Top asked as Lyra put in a swirling purple crystal while the former looked through a section of ones the size of her head.

"What do you mean?" Lyra asked the carrot farmer, who shrugged.

"After the war? I mean, the way things are going, it looks like the war will end soon with how bad things have become for Equestria. I can't see it holding or even existing in the next few months whether the Doctor does something or not," Carrot Top said with a sigh. "What do you think happens next after that? Obviously, the U.N. will occupy Equestria for several years, and a new government will be built, but what about us?"

"...I haven't thought about that," Lyra admitted as she lowered her head. "Honestly, I don't know. I can't go back to Equestria. I got nothing left there."

"Same," Carrot Top muttered as she picked up a sparkling blue crystal and put it in the box. "My parents were outside of Equestria when we teleported her. Meaning they're....d-d-dead...all I got is Derpy and Dinky, so I'm with them in whatever they want to do."

"Yeah, my parents made it clear they never wanted to see me again the last time we spoke. I don't even know if they're still alive at this point," Lyra admitted but shrugged. Truth be told, she never really was close to her parents. They were always so busy with work that they never really had a close bond. "My old friendships are gone too. Bon-Bon... she hates me, so that's out."

"Were you two a couple?" Carrot Top asked, which made Lyra blush and nearly lose mental control over her magic. "Sorry, but there was always a bet in Ponyville on whether or not you two were together or had feelings for each other. I mean, it was kind of obvious that Bon-Bon liked you-"

"Wait, really?" Lyra asked in shock.

"Seriously? Girl, that mare was so into you that it was as obvious as Spike's crush on Rarity," Carrot Top laughed, which made Lyra cover her face in embarrassment. "But seriously, did you feel the same?”

"I...I admit I found Bon-Bon attractive, but I was more into guys than girls. It never became anything more than friendship between us," Lyra admitted while rubbing the back of her neck. "Maybe if things were different, I would have fallen in love with her, but I only saw her as a close friend."

Bon-Bon had been Lyra's first true friend in quite a while. As she got older, she grew apart from her old friends like Twilight, Moon Dancer, Minuette, and so forth. When Lyra decided to move to Ponyville, she found Bon-Bon as a roommate, and something clicked between them that made her want to stay. It was like finding the other half of her that she could do other things with, and Lyra always assumed they were just best friends.

But what if it was more?

What if she fell in love with Bon-Bon?

If so, when could it have happened?

What would their future have been like?

"What about The Doctor?" Carrot Top asked with a grin. "You two are close. I mean, you've known him for a while now. Any interest in him?"

Sticking out her tongue, Lyra said, "Ugh, no! If you ignore how he looks, he's way too old and weird to be a boyfriend. He's just my friend. I care about him and all, but not like that. We're close, but not that close."

When those who had supported Lyra's views about humanity started getting arrested, she felt like she was all alone in the universe. There were no friends or family besides her, and she was hated by many while being a wanted criminal on the run. Then The Doctor saved her, showed her so much, and helped her achieve her desire to save humanity.

The moment she met him and he offered his hoof to her on that day they met, something inside Lyra knew that she could trust him.

It was always like that around The Doctor.

Even now, after all their time together, that trust was still there. You could look at The Doctor and believe him when he says he'll carry you back to the ends of time and space.

He wanted to save the world, and Lyra thought he could do it. He really was amazing in what he did, and all his actions were so noble and brave that he was like those fabled heroes she used to read about as a filly. Yes, he made mistakes and occasionally showed a dark side that frightened her, but Lyra knew The Doctor would never hurt her or anyone close to him. He was a great stallion, and she would always trust him no matter what.

"Yeah, same here," Carrot Top said before chuckling. "It's funny. We've only been together briefly, but it feels like a lifetime already. I know he said we're free to leave whenever we want, but honestly? I kinda like traveling with him. He's got this... energy..."

"That makes you want to follow him, knowing everything will be okay? Yeah, I get it," Lyra said with a sigh. She smiled warmly and thought about her beginning days with the strange pony in a blue box. "To be honest, I think I want to travel with him forever. Or at least for a very long time. I've always wanted to be an adventurer. I moved out of Canterlot because I wanted to be a traveling minstrel on the road. Seeing new places and meeting new folks. I only stayed in Ponyville because of Bon-Bon."

"Well, we do have a new universe to explore. Maybe we'll find more interesting adventures along the way," Carrot Top suggested as they got the last of the crystals and left the room. "What do you think of his theory of the Princess being mind controlled?"

“I don’t know. But if she is being mind controlled what does that mean overall?” Lyra asked as she scrunched her face in thought. “Is Princess Celestia really in control of her own actions? Or was she just pushed and always had this darkness inside of her? Is she even working with this person controlling her? I don’t know but it doesn’t matter. What matters is that we stop this war no matter what regardless of who really is pulling the strings.”

BOOM!

The girls yelped as they turned down the hall where the room of chemicals that Derpy went into suddenly exploded, and smoke was coming out of it along with fire alarms. Whistling to herself, Derpy walked out with a number of vials in her saddlebags while covered in soot. Looking at both girls with her crossed eyes, she smiled at them. "Hi, girls. I got everything."

"...Derpy, what happened in there?" Carrot Top asked, pointing to the burning room.

Turning around, Derpy looked at the room she came out of before turning back to the others and giving a sheepish smile. "Oh, that. I accidentally knocked this glowing red thing into this glowing blue thing, and it made this glowing purple thing, and then there was a big explosion. My bad."

"...I would say that I'm surprised, but I'm not," Lyra sighed as Carrot Top facehoofed.

***

Applejack had always held a belief that if you worked hard and stayed true to a good cause that you believed in, you would get good things in return.

Applejack worked hard to keep her farm afloat with the rest of her family after her parents died. There were some rough months here and there, but overall her dedication to keeping her family farm and their legacy going was rewarded with prosperity. She performed the same thing when she did her duty as an Element of Harmony for the betterment of her nation and believed in the cause of the war when they came to Earth to help humanity find a better path.

And now that hard work and devotion were bucked right back into her face.

Applejack was stubborn to ever admit she was wrong. Everypony knew it, including herself. Laying on a prison bed as a prisoner was her reward for making the bad choices in her life recently. Karma had come, and it was making it clear to Applejack that she bucked up.

The worst part of all this was that her imprisonment was done by a former friend that Applejack had greatly respected and the very Princess she worshiped and trusted her entire life.

Well, that proved that all the hard work and faith in the world was worth nothing if it was all going to crap in your face by those who abused it. Applejack sacrificed everything for Equestria because she believed in its leaders, and the leaders betrayed her at the end of the day.

The Princesses betrayed her.

Her goddesses betrayed her.

A lot of rage was going through Applejack despite her cold, stoic expression. Anger at the fact that she wasted everything on a cause that ultimately didn't care about her and ruined her family.

Big Macintosh, Apple Bloom, and Sugar Belle were safe, at least, but they could never come to Equestria again. Mostly because Applejack doubted there were no more Sweet Apple Acres to go home to.

She had no doubt the farm was already being occupied and nationalized by the crown. Even after all the money, donations, taxes, and food the Apple family had donated to it, that wasn't enough, and they would bleed it dry. The legacy of four generations of Apples was all but gone.

All that effort, time, sweat, and hard work was wasted.

And the worst of it all was part of it was thanks to Twilight Sparkle. Twilight was once a friend. Buck, she was somepony Applejack considered part of the family and treated her like a sister. And Twilight just stabbed her in the back like this.

If Applejack knew that this was how it would end, she would have snapped that bucking unicorn's neck with a buck to the face the first day they met. Even if it would mean eternal night forever by Nightmare Moon.

Of course, all that anger was pointless. She was trapped here with Rainbow Dash and Rarity and would be used against her will to cause more death and destruction.

‘Is this my punishment? Everythin' Ah did comin' back to bite mah flank?’ She thought glumly to herself.

She didn't know. And deep down, Applejack didn't care. She was just tired of everything. The fighting, the war, the chaos, the death, and so forth. She just wished she could just run away from it all.

Applejack heard the prison doors open and sighed while wondering if it was their new jailors or their meal being served. Then, she heard a voice she hadn't heard in years.

"Girls?"

Applejack's eyes snapped open, and she ran to the cell barrier as fast as her hooves could carry. She wasn't the only one, as Rainbow Dash and Rarity were doing the same thing, only with tears in their eyes. Applejack was too shocked to do the same thing, but her mouth dropped all the way down, and her heart beat rapidly in her chest. “F-F-Fluttershy?”

It was her. It really was her. Nearly a year since she left, and suddenly their friend, who they once cursed as a traitor, was there smiling at them with warm eyes. Beside her were Dinky Hooves and Flash Sentry, who stood there stoic and unmoving.

"F-F-Fluttershy, is that really you, Darling?!" Rarity almost asked in desperation.

"Yes, girls. It's me. We've come to get you out of here and sabotage the Harmony Cannon," Fluttershy said as she nodded. Flash Sentry walked over to the lever holding their barriers up before pushing it down. In a split second, Applejack found herself outside her prison, free as a bird.

Rainbow Dash was the first to rush out and wrapped her hooves around Fluttershy's neck, sobbing into her shoulder as the yellow pegasus wrapped her wings around her fillyhood friend and nuzzled her cheeks. Rainbow Dash was muttering between the gasps and the sobs, "I'm... I'm...so-s-sorry... I'm so...s-s-sorry!"

"Rainbow, it's okay," Fluttershy whispered, stroking her mane.

"No it's not! You were right! Lyra was right! I can't believe I was so stupid! I don't deserve to be a hero! Or your friend or anything! I'm... I'm..." Rainbow Dash weakly gasped before sobbing again, which made Applejack just lower her head in shame upon hearing Dash's words. Words she wanted to say but found it too painful to mutter. All she could do was let a tear drip down her cheek.

"What Dash means to say is...we were wrong...all of us..." Rarity said as she wiped her eyes. "I know this doesn't mean much, but we're so sorry, Fluttershy."

"You think that's enough?" Dinky said, glaring at them. "You realize that even if you are sorry, it will take more than that to compensate for what you've done."

"We know," Applejack said, narrowing her eyes at the younger mare. "But we'll do whatever it takes. The alicorns are the baddies here, and we're willin' to fight them now."

"Are you sure? You would be working with humans to do this," Flash Sentry pointed out. "Humans that you helped kill in the millions with the Elements."

The three winced at this and lowered their heads in shame. However, Fluttershy turned to the two and glared at them, "Flash. Dinky. Enough. This isn't the time nor the place for this. We need to get back to The Doctor."

"Are you seriously going to forgive them for everything they played a part in?" Flash Sentry asked in disbelief and anger as he glared again at them. "Even if they are sorry for it, and even if they regret it, they played a role in the deaths of millions of innocent lives thanks to giving Twilight their Elements for the Harmony Cannon and causing so much destruction."

"...We know," Applejack said as she looked up and stared back at Flash. "Yer right. We are murderers. Even if none of us wanted it as bad as it was, it doesn't change the fact we willingly gave our Elements to Twilight after she told us what the cannon was. To be honest, Ah didn't think much of it. It was just humans. Our enemies. The bad guys that Ah hated and feared. What wrong could it be?"

Applejack then sighed heavily and shook her head, looking ten years older. "Then, when Ah heard the death count, Ah suddenly felt the weighted burden of taking lives on mah back. Then Ah looked up all the deaths in the war, human and pony, which only doubled it. Ah never played any role in the war other than keepin' spirits up and feedin' the troops, but when Ah finally took action and took human lives...buck Ah couldn't look at the mirror and see who Ah was. A murderer. A damn bucking murderer. It only took Pinkie's death for me to see just how far Ah'd fallen. How we all had fallen."

She really wished Pinkie Pie was here. Heaven knows Applejack would do anything to hear the party pony just say something positive to make her have some hope for them all.

"However, that doesn't mean Ah won't make things right," Applejack said as she took a deep breath and glared at Flash and Dinky. "We bucked up. None of us will deny that. But Ah want to make it right or at least try. Even if Ah never succeed. Even if Ah'm never forgiven. Even if Ah'm going to Hell when Ah die, I still want to make it right. I want to stop this war. Ah want to do the right thing just once. Even if there is no reward for it, Ah can at least die knowin' that Ah tried in the end."

"Me too," Rarity said while nodding her head. "It's not about our reputations. It's about fixing our mistakes. Even if we can't succeed, we want to try."

"We want to be heroes again... even if we're cursed as villains for the rest of our lives," Rainbow Dash whispered as she separated from Fluttershy and smiled softly at her. "We want to be the ponies we once were before we got twisted. I want to be the Rainbow Dash that fought beside her best friends to save the day. Especially with you, Fluttershy. I...I missed you..."

"...I missed you too," Fluttershy whispered as she hugged Rainbow Dash, and the other Elements soon joined in the hug. "I missed you all."

Dinky and Flash looked at each other, their expression softening somewhat before the former sighed. "Alright, we get it. But let's deal with this after we escape from this place. Let's meet up with The Doctor and go from there."

"Yeah, he's probably already in the room of the Harmony Cannon preparing to destroy it right now," Flash Sentry said with a grin.

"Wait, how could he get in there just like that?" Rarity asked in confusion.

"The Doctor said he had a plan. Something about a paper?"

+}{+

"As you can see by my credentials, I am more than qualified for the job," The Doctor said as he held out his paper to the guard in the main room where the Harmony Cannon was being worked on by engineers and scientists.

The unicorn guard stared at it with confusion before asking, "I still didn't get any notice that you were coming. Why does Princess Twilight need an electrician again? A Royal Electrician? For that matter?"

"Well, with the Harmony Cannon being so powerful, it's quite draining for the current geo-crystalic generators that are powering the fort, and we want to make sure that constant testing and use of it will not overpower them and cause them to shut down permanently," The Doctor lied as he put his paper down and smiled. "Therefore, we're going to be preparing to hook up the Harmony Cannon to an electrical power system that will see to it that the power is not only used from an alternate source without risk to the fort's energy systems but possibly make it stronger."

"And you need us all out because?"

"I'll be working with wires and electrical currents. Don't want to shock anyone by accident. My assistants will help me shortly after they get my tools. Don't worry. It's all with Princess Twilight's permission."

The guard shrugged and nodded. "Well, your papers looked legit. So who am I to argue? I'll get everypony moving in a few minutes."

The Doctor nodded as the guard went about rounding everypony up to explain the situation. Once they all exited from the various doorways, he kissed the folded paper wallet in his hooves. "Psychic paper. Always useful."

"Hey, Doctor!" Turning around, The Doctor saw Lyra, Carrot Top, and Derpy Hooves entering the room with the crystals he requested in a box they were carrying while Derpy took off her saddlebags and presented them to the stallion. "We got everything you wanted!"

"Fantastic," The Doctor said as he took the crystals and placed them on a large steel table before getting the vials of chemicals. "This shouldn't take too long. Just gotta make these crystals soaked in the right chemicals, do a little mixing, and make some adjustments with the sonic screwdriver. Once all that's done, we should be ready to sabotage the cannon."

"How long will it take? I mean, I can't imagine Discord can keep distracting the others forever," Lyra pointed out.

"Oh, we got time. So long as nopony figures out what is really going on."

+}{+

“Just how many are there?!” Twilight shouted as she kept firing fire blast after fire blast. It had to have been nearly thirty minutes now, and the Wendigos were still flying around and giving them cold blasts.

“I don’t know, but I’m surprised we lasted this long!” Cadence pointed out as she used her magic to shield her, Twilight, and a few guards from a passing Wendigo. “How many on our side have been frozen?!”

“...None,” Twilight said but with a concerned tone. “Wait a minute. Cadence, do you remember how fast Wendigos can freeze a pony?”

“Um, no. Not really,” Cadence said with confusion.

“The fastest record of a Wendigo freezing a pony, according to the books about their abilities, is 0.7 seconds, while the longest it ever took was 1.96 seconds,” Twilight said as realization began to sink in. “We’ve been fighting these Wendigos for at least twenty or twenty-five minutes, but nopony has been frozen. In fact, the air is mostly just frigid but not chill to the freezing point needed to solidify a living body into ice.”

“...Wait a minute, if they aren’t freezing us, then that means-”

“They aren’t real!” Twilight shouted in frustration as she started building up her magic. “This is all an illusion!”

Twilight began to harness as much energy as possible around her like a glowing star. Her eye began to glow white as she flew into the air before scrunching up her body.

With a loud cry of rage, she unleashed her magic in a giant purple shockwave that spread across the entire area. Her dispelling spell instantly made every Wendigo disappear as if they were wiped from existence, and the weather immediately changed from a bad snowstorm into a calm, cloudy one with a minimum amount of snowfall. Soldiers looked around in confusion as their enemies vanished into thin air, and Princess Celestia, panting from the energy she had already used, flew down to Twilight and Cadence.

“W-What happened?! Where are the Wendigos?!” Princess Celestia demanded in confusion.

“There were never any here! This was all an illusion! We’ve been distracted!” Twilight shouted as she began looking around.

“By who?” Cadence asked.

“...Him!” Twilight shouted as she fired a magical bolt straight into a nearby rock which soon warped away and shape changed into a certain draconequus who waved his hand in greeting. “Discord!”

“Hi, Twilight! Sorry, I didn’t phone ahead. My phone bill hasn’t been paid off for the year,” Discord said with a chuckle. “You know how it is with Verizon these days.”

“Wait, if Discord is here, then that means...” Celestia realized in horror.

“It’s The Doctor! He’s here for the Harmony Cannon!” Twilight shouted. “We have to get there!”

“Yeah, not happening. See ya!” Discord said as he snapped his fingers and was gone in a flash.

“Come on! We have to teleport!” Twilight shouted as she and Celestia focused their horns on sending everypony in the vicinity to Fort Obsidian.

However, a split second later, their horns let out a burst of magical backlash that knocked them off their hooves and onto their flanks. Shaking their heads, the two winced upon feeling the whiplash of their magic being blocked against their skulls. “What happened?”

+}{+ Ten Seconds Ago +}{+

Discord appeared back in the security room where Spike was waiting for him. He sighed out of tiredness and said, "Jig is up. They figured it out."

"Good thing we got a backup plan to give us more time," Spike said as he walked to the security station they had arrived in earlier.

The Doctor said there was a chance that the plan would distract most of the guards and any reinforcements would be figured out. Not to mention there was also the chance that Discord would run out of energy before they could destroy the cannon. As such, he made a backup plan to give them more time by hacking the defenses of the Fort through the crystal's complex magical nexus network and activating a specific shield that Twilight had installed.

Twilight was extremely paranoid about anyone coming in and ruining her hard work, and The Doctor was one of them. It reasoned she would create some kind of anti-teleportation shield to prevent him from arriving, but Twilight failed to understand that the TARDIS was more advanced than just simple teleporting. It was far beyond even her brilliant mind's magical and scientific understanding. However, just because it didn't work for the TARDIS doesn't mean it couldn't work for anypony else.

Especially alicorns.

Spike pressed the right crystal button, and it started to glow green to indicate the defenses were up. Turning to Discord, he said, "Come on. We better meet up with the others."

+}{+

"No! No! No!" Twilight screamed in frustration as her hooves pounded the snow. "That bastard! He must have activated Fort Obsidian's Anti-Teleportation Shield! How?! I wrote that complex system myself!"

"Considering he was able to easily hack our communications back in Osaka, I'm honestly not surprised to hear this," Cadence said rather calmly despite her worries. She didn't care if The Doctor was here to destroy the cannon. Honestly, she'd be happy to see it turned to rubble. What Cadence did care about was if Flurry Heart was with him and the rest of his companions.

And no matter what happened, Cadance would not let Twilight or Celestia hurt her daughter if this was true.

"Doesn't matter! We're flying to the Fort now and gathering every bodied soldier we can!" Celestia shouted before her voice suddenly turned into a dark and sickening tone that made everypony freeze up in fear upon hearing it. "THE DOCTOR WILL NOT ESCAPE AND RUIN EVERYTHING!"

“C-C-Celestia?” Cadence whispered in fear as her aunt's tone was unlike anything she had ever heard. It was like hearing nails against a chalkboard while distorted in unholy words. However, Celestia didn't answer and just flew as fast as possible toward the direction of the Fort as if she were a white and yellow comet.

Cadence slowly turned to Twilight and asked, "Y-You h-heard that, right?"

"Y-Y-Yeah," Twilight answered, looking as disturbed and scared as Cadence. "I-I-I've never heard her speak like that before."

"...Something is wrong," Cadence said, an awful feeling growing in her gut. "We have to catch up to her. Can you teleport us as close to the Fort as possible?"

"I can try," Twilight said as she closed her eyes and concentrated before there was a large blink, and both she and Cadence teleported along with the troops.

+}{+

The Doctor used his Sonic Screwdriver one last time before pressing a few buttons on the computer connected to the Harmony Cannon. He was glad that Spike and Discord came when they did, as he needed their help to load the chemical-soaked crystals into the cylinder container used to house the regular Elements of Harmony. The real ones were not going to waste, however, as The Doctor happily asked Derpy to hold them in her saddlebags as they would be safer in their hooves.

It wasn't long after that Dinky, Flash Sentry, and Fluttershy arrived with the formerly imprisoned Rarity, Rainbow Dash, and Applejack, who were soon enveloped by Spike. The five friends all hugged each other with tears in their eyes before noticing the others staring at them. There was a bit of awkward and intense staring for a few minutes until The Doctor coughed into his hoof.

"Well, glad to see we're all caught up and back together again," The Doctor said as he smiled at everyone. "I must say this is a large group, but the TARDIS should be able to hold us all together once we're out of here."

"I take it that you're The Doctor?" Rarity said as she looked at him. "Hmm, not a bad outfit. But it could do with some work."

"You should have seen what he wore in the past," Lyra giggled. "He actually looked like a clown in his sixth outfit."

"Ugh, please don't remind me. I don't know what I was thinking. I blame the suffering from Regeneration effects for that one," The Doctor grumbled as he facehoofed.

"At least it's better than that eleventh outfit you wore. You looked like a geek," Carrot Top said with a snicker.

"Oi, bowties are cool," The Doctor pouted.

"Okay, can we focus here?" Applejack said, getting everyone's attention. "We already know yer here to sabotage the Harmony Cannon. What can we do to help?"

"Oh, there is no need for that!" The Doctor chirped as he pointed at the giant weapon. "Everything's set and ready. Just a few more things to do, and we'll be set."

"You sure that this is going to work, Doctor?" Dinky asked, looking up at the giant monstrosity.

"Positive! I did a similar thing with Gallus and Silverstream on a Rutan ship when they created that giant world-destroying mega railgun that nearly destroyed Equus in the year 4012," The Doctor claimed as he got out his Sonic Screwdriver. "Just need to-"

SMASH!

Everyone turned around to see the front doors get blasted open to pieces as Twilight and Cadence rushed out with armed guards.

"Doctor!" Twilight shouted with rage. "Stop right there!"

"Oh, hello, Princess Twilight. Princess Cadence," The Doctor said passively with a nod. "Was wondering if you were going to get here."

"Doctor! You will not destroy the Harmony Cannon! I will kill you if you try to stop the only weapon we have to survive against mankind!" Twilight cried out as she pointed her horn at The Doctor, who didn't look bothered by this.

Glaringly, Lyra marched in front of The Doctor and shouted back, "If you want to get to him, you have to go through me!"

"Fine! I can't even believe I was friends with you once!" Twilight shouted in disgust.

"And you'll have to go through me too!" Flash Sentry said, marching forward and standing beside Twilight, who winced upon seeing her old boyfriend. "I'm not afraid to stand against you, Twilight."

"Flash..."

"Twilight, I care about you. Even after all this and all you'd done, a part of me still loves and cares about you. And I care about what you have become," Flash Sentry said with a deep sigh. "But I cannot side with you. What you are doing is wrong; deep down, you know this. The mare I fell in love with was smart, brave, kind, and wise. This isn't you. Not at all."

"Y-You don't-"

"Twilight, enough," Spike said as he stepped forward to stand side-by-side with The Doctor. "Are you willing to go so far in your lust for revenge that you'll kill anyone? Even me?"

"S-S-Spike you don't..." Twilight shut her eyes and started to leak tears. "You don't have to...I...just come back and..."

"No, Twilight. I'm not coming back. Not until I have my sister and best friend again," Spike whispered as he solemnly looked at Twilight with pity. "I don't know what's become of you, Twilight, but this isn't you. This war has twisted you, and so has Celestia."

"No! That's a lie! Celestia-"

"Celestia is the liar!" Fluttershy screamed, which surprised all her friends as she huffed and put her hoof down. "Think, Twilight! Look around you! All of us are against you! The friends and family that love you! Do you really think we would betray you without a good reason?! Celestia used us to teleport Equestria all to this world and abandon our own to die! Every creature back home is dead because nopony is there to raise the sun and moon! We started a war of genocide, not peace! All because of her lies!"

"Equestria has always preached about peace and harmony, Twilight," Dinky pointed out as the purple alicorn began to tremble. "What kind of peace is there in invading a planet while causing its people to slowly die out from a giant deadly barrier and forcing them to convert to a form against their will or suffer an agonizing death? What harmony is there in starting a war just because they wanted to be left alone as their own selves and decide their own fate?"

"Why did we not try to find other peaceful ways of coexistence? Why go to the extreme?" Carrot Top said while shaking her head. "Celestia was always going to try to eliminate humanity, Twilight. Be it from the Conversion Bureaus or war itself, Celestia's ultimate goal has always been a world where ponies only exist. Not humans, griffins, dragons, diamond dogs, changelings, or any other creature. Just us."

"But...But..." Twilight was now openly crying as her hair was in a frizzle. Slowly the magic in her horn began to subside.

"Twilight," Applejack said, stepping forward. "We're your friends. We've been through so much, but look at what's happened to us. We're... we're not the same anymore."

"We committed a terrible crime, Twilight," Rarity whispered, closing her eyes in shame. "We've done things our old selves would be ashamed of."

"Pinkie Pie is dead, Twilight," Rainbow Dash pointed out with a heavy tone. "She couldn't accept what she did and ended her life. She knew what we did was wrong but couldn't live with it. The truth is, Twilight, we were all wrong. We're the bad guys. We're the Nightmare Moon, Tirek, Chrysalis, and so forth. We... we're the monsters this time."

"...My brother is dead," Twilight whimpered.

"And how many other brothers are dead from this war, Twilight?" Discord pointed out as he folded his arms. "How many fathers, mothers, sons, daughters, brothers, sisters, and more have died on both sides? A war that has seen nothing but utter hatred, death, and destruction on all sides. You have caused more chaos for one species than I ever did during my evil days. And I never killed anypony in all my years! Tell me, is this the Harmony and Friendship you have fought for all your life? Look around you. All of us, those you once trusted and loved, stand against you. Will you let your admiration of Celestia blind you from the truth until there is nothing left for you to hold onto?"

Twilight couldn't speak. She looked down so lost and conflicted that she looked ready to explode. With a heavy sigh, Cadence slowly walked over, put her wing on Twilight, and made her sister-in-law look up. "Twilight. Enough. It's over."

"...I...I...I..."

"Twilight?" The Doctor said as he stepped forward. "Do you know I was traveling with a mare named Sunny Starscout? She comes from far from your future. Long after you died. Equestria was separated and divided thanks to the manipulations of an evil alicorn named Queen Opaline Arcana. Earth Ponies, Unicorn Ponies, and Pegasus Ponies separated from each other, and all of them lost their magic."

Everyone was staring at The Doctor with wide eyes and shocked upon hearing about such a future. A divided Equestria? Ponies without magic? Did that mean that their efforts would ultimately be undone no matter what?

"But there was this one earth pony who believed in the tales of the old days. When all ponies worked together with Friendship and Harmony. She dreamed of being an alicorn like her precious hero from those days. A hero who stood for what was right by helping others and uniting not just ponies but all creatures with the magic of Friendship. Sunny's faith in her teachings led her to befriend unicorns and pegasi. Together they brought back the Magic of Friendship and made it even stronger."

The Doctor pointed to a stunned Twilight, who collapsed onto her haunches. "That alicorn who she loved, worshiped, and admired so much that she practically acted as her successor? That was you. But she doesn't exist anymore. She never will because Equus is gone. The future that could have been is gone. A future where the entire world united and set out to the stars. I've seen that future, but now it's gone forever. So let me ask you, Twilight. What future would you have preferred? This one? Or the one that never should have been lost in the first place? The future now where war and death linger in the air or the one where Friendship, even if it was lost for a while, never truly died?"

“....aaaaaaAAAAAAAAAAAAAAAAAAAAAHHHHHHHHH!!!!!”

Twilight fell to the floor and wailed. She wailed and sobbed. Cried and screamed. Pounding her hooves into the ground repeatedly as her emotions flooded out. In an instant, her friends were all there for her, as were Spike and Cadence. Twilight continued to moan in sorrow and shame as they hugged her, crying beside her as the truth finally pierced through her heart.

"I'M SORRY! I'M SORRY!" Twilight screamed in the middle of her fit. "WHAT HAVE I DONE?!"
Lyra just watched as Twilight, guilt-ridden and full of pain, continued to cry, yet there was no satisfaction on her face. Nopony on the Doctor's side looked satisfied. If anything, it looked painful to watch because, to the surprise of all those inside who thought they hated her, they felt some sympathy deep down for her.

Lyra slowly walked over to The Doctor and whispered, "Do you always manage to get your enemies to give up by talking to them?"

"Not as much as you think. I wish it would happen more often," The Doctor sighed heavily.

"So, we're out of danger now, right?" Lyra asked.

"No, we still need to worry about-"

SMASH!

Everything suddenly went cold as the ceiling above crumbled, and out came a furious alicorn of the sun who screamed with hatred. "DOCTOR!!!"

Discord quickly snapped to The Doctor's side and summoned an energy shield to protect him and the Time Pony as a large blast from Celestia's horn was blocked by it. Princess Celestia soon landed on the ground, growling at The Doctor before turning into a shocked and teary-eyed Twilight. "What are you doing, Twilight?! We need to-"

"You will not speak to her!" Spike shouted as he stood in front of Twilight with a growl. "You will not speak to her or anyone ever again, you lying witch!"

"How dare you! I am-"

"A traitor to everything we stood for!" Lyra shouted with hatred in her tone. "You lied to us all! You manipulated us into leaving our home world and leaving everyone to die! Didn't you! Don't deny it anymore!"

"I did-"

"Celestia!" Cadence shouted as she stood tall and brave. "This is over! Everypony here stands against you! I am, at this moment I am relieving you of your crown! You are under arrest for treason, genocide, murder, lying to the Equestrian people, and many more crimes!"

Everypony was glaring at her, but The Doctor, who was just observing, and Twilight, who just looked away in despair. Even the guards, both Equestrian and Crystal Empire, had finally seemed to know where the wind was blowing and raised their weapons toward Princess Celestia a bit with some reluctance.

"...I can't believe this," Princess Celestia said in disbelief as she looked at them all. "After everything I did! All that I've done to save you?! You do this to me?! The one who saved us all from total destruction?! I prevented our entire race from being extinct! I sacrificed everything for us, and you turn against me?!"

"What are you talking about?! Just shut up and make sense already!" Rainbow Dash screamed.

"THE SUN WAS GOING TO DIE!"

There was a sudden wave of silence as the words that Celestia had said. Some were just confused, while others were just looking in disbelief at each other. Finally, Flash Sentry asked, "W-What are you talking about."

With a heavy sigh, as if a burden had been lifted off her shoulders, Celestia closed her eyes and lowered her head. "You want to know the truth? Fine. For hundreds of years, I have had visions of the sun dying. It was going to explode into one big bang and doom us all. Rivers would be set aflame like lava. Entire nations were wiped out. Our very forests turned to ash. All I saw was death, death, and more death for so many nights I feared I might go mad."

Raising her head up and glaring at everyone, Celestia continued to defend her actions. "I tried so many methods to save the sun! I did! You think I wanted to do this?! We only had a few more years until the sun would die! I didn't want to leave our home and come to this forsaken planet of destitution, but I had no choice! There was no choice but to leave! Yes, I sacrificed all the other life on the planet, but it was them or all of us! I never wanted to kill them all, but I had to do it for the sake of my ponies! That is the burden I carry every day with this crown! Everything I do is for our survival and way of life to flourish! Even if it means lying, manipulating, and even killing, it's worth it for every single foal in Equestria to sleep peacefully at night!"

She pointed her hoof at every single one of them. "Could any of you do what I had to do?! To make that choice?! To choose between annihilation or genocide?! I had to choose the lesser of two evils, so I chose to abandon Equus for our own survival! Call me a monster if you wish but do not call me a traitor! Not when everything I did was for Equestria!"

Nopony said anything for a long time.

Until...

"...So that's how they did." Everyone turned to The Doctor as he slowly stepped forward and stared at Celestia with narrow eyes. "That's how they manipulated you. Of course. Something so simple. Affecting the dreams of someone. Showing them the same images of disaster and destruction repeatedly. Such a thing would slowly corrupt your sanity and weaken your mental defenses so they could start influencing you. As your psyche began to fail, they started to get inside of you personally. I wonder how much of you they took control of and how much they have now?"

"Umm, Doctor? What are you talking about?" Derpy asked, with one eye focused on him and one eye focused on Celestia.

"...Everypony, I know this will be hard to believe, but I've been suspecting this ever since Spike and Flurry Heart told us about the black eyes. I have always wondered why Celestia would do something like this when it goes against all reason, but now I have it," The Doctor growled with such rage that it surprised a few of those who knew him. "We've all been deceived. All of us. Humanity. Equestria. Even myself. We've all been manipulated. This entire war? It was all for someone else's benefit!"

"What are you talking about!" Celestia demanded.

"Celestia," The Doctor said. "You claimed that the sun was going to die. But I am a time traveler and can tell you now that never happens for millions of years! The sun was young and healthy! It doesn't die for a very long time!"

"L-Lies you are-"

"I'm a Time Lord!" The Doctor screamed as he slammed his hoof to the ground in such a loud and haunting tone it made everyone step back with their spines tingling in their backs. "I have seen the birth and death of the universe! I have crossed the boundaries of time and space! I have witnessed empires rise and fall! Watched as species of endless numbers live and die! I have been to countless realms and dimensions beyond the natural state of our own reality! Past, Present, and Future are all available to me! I ride the threads of Fate and turn the wheel of Destiny. I have been to Equus since the day it was first made to the day it breathed its last, and I tell you now, Celestia, that the vision you speak up never happens!"

Suddenly, Celestia went pale as a ghost. Her mouth dropped, and her eyes widened. A look of sudden realization hit not just her but also everyone in the room as they realized The Doctor was right. Everypony, even those who never joined him, learned and were told he was a time traveler. Those who were among his companions had seen it firsthand. If The Doctor was still visiting Equus long after the supposed date of the so-called destruction of the sun was to happen...

Her visions were a lie.

The entire war was a lie.

Everything Celestia had done was for nothing because what she feared would never come to pass.

Which meant that their entire involvement on Earth was never supposed to happen in the first place.

All of those deaths, all of those battles, the suffering and so forth.

It was all never supposed to happen.

"...I...I...What...I don't...the visions..." Celestia muttered in disbelief as she began to step back in shock. "No...no, I saw...I was told...he told me...wait...who...I...Ugh!" She started clutching her head and shaking. "Ugh! Ugh!"

"C-Celestia?" Twilight asked, slowly standing up.

"Wh-I...I..It hurts! It hurts!" Celestia started screaming as her eyes began to glow a sickly black, making everyone back away.

"There you are!" The Doctor shouted as he glared at Celestia. "No more lies! Stop hiding behind the curtain and reveal yourself! Who are you?!"

"....I suppose it's time we ended this charade, Doctor."

Suddenly, a wave of pure dark, and evil energy erupted from Celestia's body. That nearly wiped everyone off their hooves. Gasps were given as everybody, even The Doctor and Discord, felt their souls turn to ice from the sinister and depraved energy coming from Celestia's body. The power behind this force could only be described in one word.

Evil.

Pure evil.

The Doctor watched in horror and soon snarled as the energy began to form above Celestia, who went limp like a puppet without strings. "I should have known. You. Of course, it was you. Of all the beings twisted and dark in the galaxy, only you would want this sort of chaos and destruction. It suits you, doesn't it?"

"D-D-D-Doctor, what's going on?!" Lyra shouted in fear as she felt her entire body shiver at the pure dark being emitting out of Princess Celestia like a specter.

"The real villain behind all of this, Lyra! Princess Celestia was manipulated into thinking that the sun would die by this evil force that stands before us! Sending her false visions and preying on her fears, he slowly began to influence and control her!" The Doctor shouted in both fury and caution. "All the deaths, suffering, and pain both planets have felt are because of him! He's the real mastermind behind everything!"

"But who is he?!"

"One of my oldest enemies and one of the most dangerous. A god-like being of unimaginable evil power. The source of all darkness and chaos in our universe," The Doctor muttered as he narrowed his eyes. "The residents of E-Space call him the Night Hunter. The Draconequus called him the Soul Stealer. The Star Changelings call him the Great Demon of Darkness. And in Equestria's oldest tales, he is even called The Father of Shadows. But there is only one true name to his being..."

The concept then began to finalize its form in an astral project, taking that of a robed giant vulture of pure black wings and dark purple eyes of darkness. It loomed over them with its enormous wings and smiled sinisterly with its beak before letting out such bone-chilling laughter that fear engulfed all their hearts, and they stood in terror before what could be the human concept of the Devil in proper form.

And then the Doctor gave him his true name.

“The Black Guardian.”

Author's Note

All non-old school Doctor Who fans go..."WHO?!"

Okay, so The Black Guardian is a villain the 4th and 5th Doctor faced during their years and hasn't appeared in the TV series ever since (though he has appeared in additional material like comics, short stories, and radio adventures.)

The Black Guardian, also known as the Guardian of Darkness and Chaos, is the anthropomorphic personification of the forces of evil in the universe with his brother, the White Guardian, being the one for Light, Order and Good. He was basically a powerful deity like God whose power was in check with the White Guardians as neither could be more powerful then the other as they were each their own antithesis not that the Black Guardian hasn't tried to become more powerful to rule or destroy the universe since its in his very nature to do so. There is a lot more backstory to him, but that's all you really need to know basic wise.

A lot of people believed it was going to be The Master, but I wanted to avoid using him since that was too obvious of a villain and wanted to use a classic one. I still am going to have the Daleks and Cybermen/Cyberponies as part of the villains, but The Black Guardian is our main one. As for the vulture appearance, that's based on his outfit where he wore a vulture's head https://doctorwhoworlduk.com/wp-content/uploads/2019/01/begene.jpg

Special thanks to zelkova48 for helping me edit this.

As always feel free to help at the NegotationsVerse TV Tropes Page were we do have a Regeneration folder that could use some tropes added in :)

Regeneration Part 14

“Run.”

-The Ninth Doctor

+}{+

The Black Guardian.

Also known as the Guardian of Darkness and Chaos.

The living personification that represented all evil in the universe.

One of the Doctor's most dangerous enemies in his life, though he had only faced him both during his Fourth and Fifth incarnations. The last time was during the "Enlightenment" incident when he had Tegan and Turlough as his companions. A being of near godlike power, though limited thankfully by the existence of his brother, The White Guardian, who was his opposite. So long as the two brothers existed, neither could overcome the other. Not that the Black Guardian hadn't tried to do so many times before.

For the Doctor, it was a bad memory that had returned to haunt him. For everyone else they were staring at what had to be the worst evil they had ever felt in their entire lives. Even Discord, powerful as he was, was sweating bullets as he stared at the possessed Celestia while the image of the Black Guardian's avatar glowed above them. Nopony knew what to do or even say. They were still trying to process what had just been revealed. All this time, for who knows how long, Princess Celestia had been manipulated by a great evil deity that had warped her mind into believing a lie. A lie that caused them to abandon their world, killing all lives on it while starting a war on this one that ended so many more lives.

Celestia, as well as The Black Guardian's avatar, grinned before speaking. "We meet again, Doctor. It has been quite a long time, hasn't it."

"Not long enough," The Doctor growled in disgust and caution. "How long have you been processing Princess Celestia?"

"Oh, I've been inside her since her sweet little sister went insane and was banished to the moon. Of course, I never did this originally, but I am beyond the laws of Time and Space. I am a god of great power. Entering into her mindscape and slowly lying in wait was easy. There was so much darkness inside her that she hid from the world. She puts on this brave face of being a wise and kind leader of great noble virtue, but she is a scared and angry little girl who wants her mommy and daddy back."

"You realize what you have done?! You have completely changed the entire timeline of the universe by doing this!" The Doctor screamed in anger.

"Do you think I care?" The Black Guardian snorted. "I care not for what happens in our universe. For I have a new one that I shall take control of. A fresh and young one that I can shape into my own desires without you or my annoying brother to stop me from creating a galaxy of chaos!"

"Not even you can transport yourself across dimensions like this!" The Doctor shouted as he ran the calculations. "You are tied to your brother by your bond. You cannot leave unless..."

The Doctor's eyes widened. "Unless..."

The Black Guardian grinned. "Oh yes, Doctor. Right now, my true self lies in the former world of Equus. Dead and abandoned by the ponies who left everyone to die slowly. But here, Celestia, who I possess, is also me in this universe on this planet. I have festered long enough in her body that I am also her to an extent."

"And you plan on using your two selves to create a link that will unite both. Dragging the two worlds and making one version of both worlds and a single version of yourself. It would cause both worlds to be destroyed, and yet you would be able to successfully bring yourself over with all your power," The Doctor whispered in horror as every creature stared at The Doctor in horror upon hearing this. "How?!"

"I am powered by chaos, Doctor. What's more chaotic than a war?" The Black Guardian laughed. "All this death, suffering, and chaos has fueled my ritual. My key to summoning my true self to this dimension. I am close. So close to my goal, but I need more war! More death! More destruction!"

"So why help the ponies against humanity?! Why them?!" The Doctor demanded.

"Tch, I didn't care who won the war. Humans. Ponies. They can destroy each other for all I care. Death is death in the end. It's not for whose blood I care for. It's that blood is spilled either way," The Black Guardian answered.

"...You mean to tell me...that you have been using us..." Lyra muttered while shaking with both horror and anger. "Our families, our friends, our own children! Along with the humans?! Just to fuel your stupid ritual?! And you require us all to die?!"

"Pretty much," The Black Guardian said unapologetically. "And what good little pawns you've all been for me. Dying in droves for your Princesses. Wiping out human cities. It's been some of my best fun in centuries."

"You....you..." Rainbow Dash couldn't even find the words to insult. It was clear that the Black Guardian was a monster. No, he was a demon. A true god of evil that made all the past villains she and her friends had faced look like kittens in comparison.

"...Why?" Fluttershy whispered with tears in her eyes. "Why do such a thing?"

"...Because I can. And I just want to. And I love the idea of creating my own universe in my image," The Black Guardian laughed sinisterly without any remorse.

"I really should be surprised by an answer like that, but considering it's you, I am not," The Doctor growled.

"So all of this?! The war?! The Conversion Potions? All of it was your design?!" Flash Sentry growled in anger.

"Well, I can't take all the credit. I might have manipulated Celestia into coming into this world because I knew war would come eventually since it's both your natures, Equestrian and human, to be xenophobic to other lifeforms," The Black Guardian answered. "But the barrier I didn't see coming, nor Celestia using it to take over land while creating the Conversion Potion. Yes, I nudged her a bit here and there, but all that was her choice. I only controlled her when she started thinking outside of how I wanted her to. Especially when I learned The Doctor had arrived."

"We still wouldn't be in this mess if it wasn't for you tricking her!" Spike growled.

"Perhaps, but so what? I got what I want either way? Do you think I care about you, pathetic mortals? You are nothing but insects to me," The Black Guardian hissed.

"But why Equus?! What that world?" The Doctor demanded.

The Black Guardian snarled and glared at the Doctor with hatred in his eyes. "To spite you! To make you feel pain! Time and time again, you have stopped me and my plans, so I choose Equus as a means of revenge. I wanted you to suffer knowing that the planet you care about was gone and destroyed, but of course, you had to be here to try and ruin everything."

"And I will do that. I will stop you," The Doctor vowed.

"Oh, not this time, Doctor," The Black Guardian said. "This time, I will finally win. Not even you can stop me."

"You seem to fail to realize that there are more of us than you, foul creature," Cadence stated as all the guards got their weapons ready while others charged their horns, including Cadence. "You will release Princess Celestia and surrender to us now!"

The Black Guardian grinned. "Who says I am alone?"

"EXTERMINATE!"

A red laser blast went off, and one of the Royal Guards screamed as he was hit by hit. His body glowed red as his skeleton could be seen, much to the horror of everyone, before he fell down dead with a painful look on his face as the last thing he would ever do.

"No..." The Doctor whispered in horror.

A Dalek slowly came out of the shadows. "NONE OF YOU WILL MOVE OR YOU WILL BE EXTERMINATED!"

"A Dalek!" Discord screamed in terror as he fell to the floor. Crawling away, images of his world's destruction flashed in his mind. "No! Nononononono! Keep it away!"

"Protect the Princesses!" One of the Royal Guards cried out as it charged at the pepper pot-looking tin machine and a few others.

"No! Don't!" The Doctor screamed, but it was too late.

The Dalek fired its weapon multiple times, each hitting a Royal Guard that caused the same effect as their comrade. They died before they knew it, as nothing could protect them from the energy weapon. A few unicorns fired magic, but to their shock, a green energy shield enveloped the Dalek, which took the blows, showing it was no worse for wear before it finished them off.

"EXTERMINATE!" The Dalek shouted before firing its weapon at the last scared Royal Guard, who screamed in agony before falling on his back, his corpse smoking from the blast that had eradicated his insides.

Soon, hidden passageways in the area opened up and more Daleks appeared, each ordering everyone to stay where they were or be exterminated as they aimed their weapons at the surrounded heroes. Fluttershy was doing her best to comfort the scared and panicking Discord, who was muttering to himself repeatedly. His past trauma of his people being eliminated by the Daleks sent him to a near breakdown.

"ALERT! SCANS INDICATE THAT THE ELIMINATED SPECIES KNOWN AS DRACONEQUUS IS IN THE PRESENCE OF PLANET LOKINA! ACTIVATING DEFENSES TO NEUTRALIZE THEIR REALITY-WARPING MAGIC!"

From each of the Daleks, a few black spheres on their body were removed and started floating around them and glowing blue. Discord's body began to shiver and slowly turned gray as he started coughing uncontrollably. Fluttershy looked at her best friend and asked what was happening.

"The same thing...they did to my people... they're cutting off...my access to...reality weave... can't...use powers..." Discord coughed in a panic.

"You see, Doctor. I am capable of learning from my mistakes. I realized that one of your advantages was having companions that helped you stop me. I decided to get some help of my own. Some of your worst and most evil of enemies," The Black Guardian said with a smirk.

"Figures. Evil attracts evil," The Doctor snarled in disgust as he saw his worst and most hated enemies in front of him. He turned to a Dalek and narrowed his eyes. "If you think your past defeats by me were bad? Wait until I show you my wrath for what you have just done."

"WE ARE NOT INTIMIDATED BY YOU, DOCTOR! YOU ARE SURROUNDED BY THE SUPERIOR DALEK RACE! YOU ARE THE ENEMY OF THE DALEKS AND WILL BE EXTERMINATED! YOU AND ALL OF THOSE YOU CALL FRIENDS WILL BE EXTERMINATED FOR THE DALEK RACE AND THE BLACK GUARDIAN!"

The Daleks prepared to charge their weapons as everyone gulped, but The Doctor raised a hoof and walked forward. "Wait! Wait! Wait! One second! Got something to ask!"

"And what is that, Doctor? Mercy?" The Black Guardian asked with amusement.

"Actually, just this question," The Doctor asked as he looked at the Black Guardian. "What is your big plan to wipe out so many lives?"

"Simple. I plan to use the Harmony Canon on both sides. The loss of life it can deal with each blast is beyond what I expected, and I have Twilight Sparkle to thank for that," The Black Guardian said.

Twilight herself couldn't help but wince and look down in shame that her actions gave the Black Guardian the means to complete his plan. The look on her face showed such misery and brokenness that it was a surprise she wasn't already sobbing on the ground despite the situation. Her friends and Spike were doing everything they could to help her up, but she was near lifeless with guilt already.

"Well, too bad you won't be using it. You see, I sabotaged the canon already," The Doctor said with a smirk as he motioned to it. "Dosed it with a few chemicals-based crystals that would destroy the little destructive beam quite well."

"ALERT! SCAN INDICATED THAT A DESTRUCTIVE CHEMICAL AND MAGICAL REACTION IS PRIMED FOR ACTIVATION ON THE HARMONY CANON! REQUIRES ACTIVATION, HOWEVER, TO CAUSE THE BREAKDOWN OF CHEMICALS!"One Dalek said.

"Ah, yes, but there is also another way. It's a bit more explosive, but it also does the trick! Want to know what it is?" The Doctor asked with a grin.

Realizing that The Doctor planned to escape, the Black Guardian shouted, "STOP HIM!"

"Sonic vibration!" The Doctor screamed as he aimed his Sonic Screwdriver and activated it.

In an instant, the Harmony Canon exploded, and everyone ducked for cover as smoke, debris, and lose magic was sent flying. Wild magical fire was spread everywhere, and some landed on the Daleks, who were setting a flame. Screaming, they drove around, firing their weapons in the chaos that bounced around the area thanks to the reflective crystal coating of the base. The other Daleks demanded their fellow Daleks control themselves as the Black Guardian protected himself with a black energy shield.

Everyone else had also either activated their own shields, got behind said shields, or were lucky enough to dodge the rumble. The Doctor got up and screamed, "EVERYONE! RUN TO THE TARDIS! NOW! JUST RUN!"

The others didn't need to be told twice, and everyone made their way to the various exits, but they separated from each other in the chaos of all that was happening.

The Doctor, Lyra, and Flash went one way. Derpy, Dinky, and Carrot Top went another way. Cadence was nearby to help Fluttershy carry Discord up his feet and rush with him in another direction. Finally, Spike, Rarity, Applejack, and Rainbow Dash made for the last entrance possible.

Twilight was going to join them when she was suddenly pulled away by a dark force that wrapped around her and began to electrocute her. "GAAAAHHHH!"

"YOU ARE NOT LEAVING ME JUST YET! I NEED YOU STILL!" The Black Guardian screamed as he made Celestia hold onto Twilight with her magic and weakened her significantly by combining it with his dark powers.

"Twilight!" Rarity, Applejack, and Rainbow Dash screamed in horror.

"No!" Spike shouted as he flew forward, determined to save her, but a Dalek blasted him in the wings and sent him crashing down. He growled and breathed fire at the Daleks, blocking them from coming near him as he used his dragon strength to pick one up and smash it into another.

"ALERT! UNDER ATTACK! UNDER ATTACK! ALERT!"The Dalek screamed as he was smashed again like a battering ram.

"SPIKE! GAAAHHH! JUST!!! GUHHHH! GOOOO!!!" Twilight screamed as the Black Guardian wrapped her in a dark magic cloak, and she disappeared.

"No! I-GAHH!" Spike shouted as a Dalek hit him in the leg. He looked up in horror as the Daleks surrounded him.

"EXTERMINATE!"

The ponies all screamed as five Daleks fired at Spike, who yelled in agony as the blasts hit him full force. His dying cries ended when he fell face forward, eyes shut and motionless.

"SPIKE!" Screamed Rarity, Applejack, and Rainbow Dash in horror as the dragon they once called friend died before their eyes.

"...Spike..." Twilight whispered in horror as she felt her soul nearly leaving her. Her little brother. The one she was so close to...was gone. Images of the fight she and Spike had echoed in her mind. All the horrible things they said to each other. That Twilight screamed at him in rage and sorrow.

Never again would she speak to him now.

Or apologize.

"....you....you...." Twilight's eyes glowed with rage as she let out a large burst of magic that pushed everyone but The Black Guardian back. "I'll KILL YOU!"

Spell after spell fired from Twilight's horn, tearing the room apart as Daleks were destroyed in the crossfire. Their shields could not handle her grand power and screamed as they were evaporated by the wraith of the Princess of Magic. The Black Guardian just sat there, protected by his dark powers, as Twilight continued to scream with grief and rage over everything. Her mentor is being used and manipulated. The losses she had suffered. Her own guilt over the monstrous things she had done. Twilight just let it all out like a goddess of rage and hate.

The entire area was collapsing, but Twilight didn't care. Nothing mattered anymore. Nothing but the destruction of those who have hurt her.

"Twilight!" Rainbow Dash shouted as she prepared to charge forward, but Applejack grabbed her by the tail. "Let me go!"

"We gotta move, Dash! Or we're dead!" Applejack screamed as the place continued to collapse. "Come on!"

"But Twilight-"

"She's lost it, Dash! We gotta move!" Applejack shouted, but it was evident in her eyes she didn't want to leave.

"...BUCK!" Dash shouted as she followed the others down the hallway entrance as it collapsed behind them.

+}{+

"Tell me you have a plan to deal with this Black Guardian person!" Lyra screamed as she, The Doctor, and Flash ran down the collapsing halls of Fort Obsidian. They could hear Twilight's agonizing and rage-filled screams even as they continued to move as fast as possible.

"Or these Daleks!" Flash shouted as he nearly bumped into a fleeing guard. Everypony was fleeing for their lives. Warnings and alerts were being sent to evacuate all over the base. The sounds of "Exterminate" and death screams were heard in various locations, proving there were more Daleks in the area.

"No, but we need to focus on escaping right now!" The Doctor shouted as he led them forward, using his Sonic Screwdriver to get any door in their way to open. "No matter what, we must run to the TARDIS! Hopefully, the others will make it there too!"

Just as he opened another door, Lyra was suddenly tackled off her feet and thrown down. She shook her head before gasping upon seeing a crystal blaster focused on her head and the one holding it. "B-B-Bon Bon?"

"That's Agent Sweetie Drops, traitor." The Earth Pony growled as she focused her crystal-powered firearm on a shocked Lyra. The Doctor and Flash went to move to stop her, but she glared at them. "Move, and I blow her head off!"

The two stallions looked at each other and winced before slowly backing up. The Doctor glared at her. "Hurt her, and I will make you regret it."

"Shut up! I am in control here!" Sweetie Drops hissed. "What did you do?! Where are the princesses?!"

"We didn't do anything, I swear!" Lyra shouted. "Bonnie, listen! We nee-"

"Don't call me that!" Sweetie Drops screamed as she glared down at Lyra. "All this time... I've wanted to see you again...to look you in the eyes and tell me how much you hurt me. Not only did you leave me, but you betrayed our home! For those humans?!"

"Bon-Bon...listen to me..." Lyra bit her lip, and a small tear dripped down her cheek. "I'm sorry...you were my best friend, leaving you was hard...but I had to do the right thing. I know you were hurt-"

"Hurt?! You wounded me! I cared about you! I loved you!" Sweetie Drops shouted, which made Lyra's eyes widen. "I thought I could have a normal life with you! A best friend! Maybe a marefriend if you felt the same way! The two of us were happy, and I could move on from my past in service to the crown, but you ruined everything! Everything that has happened to Equestria is your fault, Lyra Heartstrings!"

Tears from Sweetie Drop's rage-filled eyes fell onto Lyra's shocked and hurt face. "Bonnie..."

"You choose them over us...your own kind..." Sweetie Drops sobbed. "...You choose them over me."

Sweetie Drops then glared at The Doctor. "You choose him over me!"

There was a long silence between the group as Lyra closed her eyes and sighed. "I'm sorry, Bonnie. But I had to do the right thing. Even if it meant losing your friendship. If I had a choice between you and the right thing...it would always be right."

"...Then I will do the right thing and kill you here and now!" Sweetie claimed, and she was about to fire when suddenly the sound of stomping appeared. Not just any stomping you would associate with hooves but steel. Everypony looked up as something was coming behind the hall where smoke and debris were. A large amount of something. Moving in unison like a legion of soldiers.

From the smoke, they came. Ponies in some kind of metallic form that made them look like robots in a sci-fi movie, but more advanced and moving with large weapons attached to their hooves. Flash saw the Doctor's mouth drop and sighed. "More of your enemies?"

"...Cyberponies," The Doctor whispered in horror.

Sweetie Drops, scared and confused, backed away from Lyra and held her Crystal Blaster up. "Who are you! Identify yourself!"

The Cyberponies continued to move without stopping.

"In the name of Princess Celestia, you will stop!" Sweetie Drops screamed as her hooves shook. When they still refused, Sweetie fired her crystal blaster. To her shock, the blow didn't even phase the Cyberpony she aimed at. It just took the impact and continued to move as if a fly had landed on it. She fired repeatedly, but there was no luck in the blows.

Finally, one of them raised their hoof and fired a hoof blaster. Lyra watched in horror as Bonnie was hit in the chest, gripping the burned, melted plasma-like wound on her chest with wide eyes. "Bonnie!"

She grabbed the falling ESS agent, who coughed up blood and stared at Lyra with fading eyes. She tried to say something, but Sweetie Drops could only cough before going limp. Her eyes widened and empty of life. "Bon-Bon! Bon-Bon!"

"Capture the Equestrians for cyberconversion. Delete The Doctor,"The Cyber Leader said as he pointed to the group.

The Doctor noticed that some pipes were sticking out of one of the walls nearby that was damaged from the collapsing infrastructure of the base and pulled out his Sonic Screwdriver. Activating it, he caused the pipes to burst, causing a wall of steam to prevent the Cyberponies from seeing them. Flash grabbed a crying Lyra and had to drag her off her deceased former best friend. The three ran as fast as they could down the hall as the Cyberponies continued to chase after them, smashing their hooves over any corpses in their way without care, including Sweetie Drops.

+}{+

Cadence felt like her entire world had just been turned to ash. Her aunt had been manipulated by some apparent dark alien god that was the manifestation of all evil in the universe. Her homeworld was gone, and all the creatures with it. Celestia was processed, and she could hear her sister-in-law fighting to the death against the abomination possessing the Princess of the Sun. She had seen alien creatures with advanced technology kill her best guards as if they were bugs. And now she was helping two former traitors escape from the collapsing base.

"How much father?" Cadence asked as she helped Fluttershy by using her magic to carry a weakened Discord.

"We're still a distance away," Fluttershy answered as she winced upon seeing the dead bodies of various ponies. Victims of the carnage the Daleks were causing or the falling debris. One head was smashed under a large piece of rubble, and the Element of Kindness felt like she would puke.

"Leave me..." Discord moaned as he winced. "I'm useless and slowing you down...just go..."

"No! Not without you!" Fluttershy shouted as she forced Discord to look at her. "We're in this together. Always."

Cadence looked at the two and felt the love emanating from them. She couldn't help but smile at Discord, who looked at Fluttershy with his feelings. She had always suspected something was between them, but the Spirit of Chaos kept his emotions hidden from her senses. Now that he was so weak, it couldn't be held back anymore. He was so in love with Fluttershy, and Cadence could suspect the feelings could be returned if given time.

"SEARCHING FOR SURVIVORS! EXTERMINATE ALL EQUESTRIAN LIFE FORMS!"

"They're coming..." Discord whispered in terror.

Cadence looked in the direction they came in and toward the two she used to call friends before deciding what to do. "You two go. I'll buy you time.'

"What?! Cadence, no! According to the Doctor, the Daleks are one of the most evil creatures in our galaxy! You can't fight them! You'll be killed!" Fluttershy shouted.

"I know..." Cadence said with a heavy sigh. "But I have done so much wrong. Made so many mistakes. At least I can die doing something right. Giving you more time to escape."

"What about Flurry Heart?" Discord asked.

"Tell her that I am sorry. She was right about everything. And she'll be a great leader," Cadence said with a smile at them. "Tell her that both I and her father love her. And that we will always be watching her."

The two stared at the Princess before realizing that there was no changing her mind. They hurried off as fast as possible. Cadence waited until they were gone before taking a deep breath. "I'm coming, Shining Armor."

She lit up her horn and flew forward as the Daleks appeared. “FOR THE CRYSTAL EMPIRE! FOR EQUESTRIA!”

“EXTERMINATE!”

+}{+

The Doctor, Lyra, and Flash arrived outside the room where the TARDIS was located and relaxed upon seeing it still there. Flash looked around in a panic. "Where are the others?!"

"Guys!" The others turned to see Discord and Fluttershy rushing towards them. "Thank goodness we found you."

"Where's Princess Cadence?" Flash asked, but the saddened and regretful looks they gave spoke their answer. "...Damnit."

"Are my friends here? What about Derpy, Dinky, and Carrot Top?" Fluttershy asked.

"LOOK OUT!"

The five of them looked in one direction to see a Dalek flying around on their thrusters, screaming as, for some odd reason, Derpy was riding it on top and doing her best to keep control. The others ducked as the Dalek flew above them. Derpy tried to keep herself on it while her flank was pressed against the eye socket of the Dalek.

"ALERT! ALERT! VISION IMPAIRED! FEMALE EQUESTRIANS BACKSIDE IS OBSTRUCTING VIEW!"

"Hey! My rump isn't that fat! Woah!" Derpy shouted as it fired its blaster, which bounced around the crystal reflections of the area. She fell off and landed on her back as the blast reflected back to the Dalek, who screamed upon being hit by its own attack and blew up before collapsing into a heap of ruin. Derpy's crossed eyes observed the destroyed Dalek. "Oops, my bad."

The others rushed over and helped her up just as Dinky and Carrot Top arrived, looking relieved to see Derpy okay. Dinky ran around and hugged her mother as The Doctor looked at Carrot Top and asked, "What happened?"

Carrot Top opened her mouth before closing it and shook her head. "Forget it. You don't want to know."

"Hey!"

They turned around to see Rarity, Applejack, and Rainbow Dash heading towards them as Rarity looked at them desperately. "Tell me you have a way out of this place!"

"Right! Follow me!" The Doctor shouted.

"Wait, where's Spike?" Lyra asked, but the saddened look on all three of them as Rainbow Dash kicked a nearby wall in frustration answered that. "No...not him too..."

"Him too?" Applejack asked as she realized that Cadence was missing. "Cadence?"

"...Sacrificed herself for us," Discord muttered in sorrow. "Twilight?"

"...We don't know..." Rainbow Dash growled bitterly.

Everyone just bowed their heads in sorrow for their losses as those they had known for years were gone. In a single day, two or three close friends were lost. They had all faced evil together so many times but never suffered a single loss of life until now. Lyra looked at The Doctor and asked, "Who is...Who is The Black Guardian? What does he want? Why is he doing this?!"

The Doctor opened his mouth to explain, but the sounds of "Exterminate" and "Delete" echoed in the halls. "I'll explain everything! To the TARDIS! Now!"

The Doctor opened the doors to the TARDIS, and everyone rushed inside. The three former Elements of Harmony stood in awe upon seeing the inside for the first time as the doors closed behind them and The Doctor went to work.

"What in tarnation?" Applejack scratched her head.

"It's bigger on the inside..." Rarity gasped in awe.

"...then it is on the outside," Rainbow Dash finished for her.

"You'll get used to it. Now let's get out of here!" The Doctor said as he activated the TARDIS.

The Daleks and the Cyberponies watched as their number one enemy's vehicle escaped them by disappearing. They looked at each other before returning to sweeping the rest of the base for survivors while informing their fellow comrades of The Doctor's escape.

+}{+

The Black Guardian, entirely in possession of the body of Princess Celestia, smirked at the unconscious and near-broken body of Twilight Sparkle. She had fought well with her rage and anger, but in the end, she was nothing. A powerful alicorn she might be, but nothing compared to a god like him. He stared at the rubble of the area as the Daleks and Cyberponies took away the corpses of the dead to be rid of them. However, the one thing that caught his attention the most was the destroyed Harmony Cannon. It was in pieces and broken beyond repair, much to his frustration.

"Report," The Black Guardian said to the nearest Dalek.

"WE REPORT THAT 96% OF ALL EQUESTRIAN STAFF ON BASE ARE DEAD OR CAPTURED! THE REMAINING ONES HAVE FLED OUTSIDE!"

"Don't bother pursuing them. They will have nowhere left to run, and the cold can kill them off," The Black Guardian answered. "Proceeded with the backup plan. Prepare the invasion forces in the Crystal Empire, Geneva, and Canterlot."

"I OBEY!"

The Dalek headed off while the Cyber Leader reported to him next.

"The Doctor and his companions have escaped."

"Disappointing, but I'm glad this isn't easy. Crushing the Doctor wouldn't be sweet if it was just done here and now," The Black Guardian said with glee. He wanted the Doctor to beg for death before him and derive him of hope before ending his existence.

"What of the Harmony Cannon? Without it, your plan cannot succeed," The Cyber Leader pointed out.

"The plan is merely delayed. All we need to do is build another one," The Black Guardian said as he looked at Twilight's body with a smirk. He might have lost the cannon, but he still had the one who built it and could even make it better. "Tell me? Can you cyberconvert an alicorn?”

"In theory."

"Time to test that theory then," The Black Guardian said with a smirk. "Convert Twilight Sparkle into a Cyberpony that will obey my will. And order your forces to join in the invasion plan with the Daleks. Let's see if we can make Cybermen, shall we?"

"Excellent," The Cyber Leader said as they walked away.

The Black Guardian couldn't help but smirk at the coming chaos.

"Let us see the ruination of an already broken world."

Author's Note

Yeah, shit got real. This is the part of any Doctor Who episode where the villains make great strides. And it's not over yet folks.

As always, please help out at the NegotationsVerse TV Tropes Page: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 15

“You can always judge a man by the quality of his enemies!”

-The Seventh Doctor

+}{+

The TARDIS was deathly quiet. Very, very quiet. The Doctor couldn't blame them. What they had seen was terrible. A terrible tragedy that had rocked all their foundations while also taking from them essential friends that had been in their lives for years. The Doctor himself was also filled with sadness as well as rage. The Black Guardian. The Daleks. The Cyberponies. Three of his worst enemies were working together to cause chaos and death on an unforgivable scale. The loss of life not just on Equus but also on Earth had wounded his heart as he thought about all the innocent lives that have suffered thanks to the works of a madman with the power of a god.

He looked over at the others from the console of the TARDIS. All of them were in a state of shock and grief. Discord was barely drinking the tea that Fluttershy and Derpy had made him as he drifted between a blank stare and sobbing in silence. No doubt the traumatic memories of his homeworld being ravaged and destroyed by the Daleks were playing endlessly in his head. And now they were playing another role in destroying not just one species but two. The Doctor's mind drifted to a time in his fourth self when he had a chance to destroy them for good but hesitated...

“Well, what are you waiting for?”

“Just touch these two strands together and the Daleks are finished. Have I that right?”

“To destroy the Daleks? You can't doubt it.”

“Well, I do. You see, some things could be better with the Daleks. Many future worlds will become allies just because of their fear of the Daleks.”

“But it isn't like that.”

“But the final responsibility is mine, and mine alone. Listen, if someone who knew the future pointed out a child to you and told you that that child would grow up totally evil, to be a ruthless dictator who would destroy millions of lives, could you then kill that child?”

“We're talking about the Daleks, the most evil creatures ever invented, you must destroy them! You must complete your mission for the Time Ponies!”

“Do I have the right? Simply touch one wire against the other and that's it. The Daleks cease to exist. Hundreds of millions of people, thousands of generations can live without fear, in peace, and never even know the word Dalek.”

“Then why wait? If it was a disease or some sort of bacteria you were destroying, you wouldn't hesitate.”

“But if I kill, wipe out a whole intelligent lifeform, then I become like them. I'd be no better than the Daleks.”

He still didn’t know, to this day, if he made the right choice. Some of The Doctor’s regenerations agreed with the decision, and others didn’t. So many lives could have been saved from the Daleks, but how much good would not have happened because of them? Do I have the right?

The Doctor then turned to Lyra, who was looking at the wall in sorrow. Tear marks were dried on her face as Flash was comforting her with some marks of his own. Both had lost important ponies to them just moments ago. Lyra had lost her former best friend to the Cyberponies, and Flash had lost his ex-marefriend, who was no doubt either dead or kept alive in a terrible condition for the Black Guardian’s plans. Considering how dangerous and influential the Black Guardian could be, The Doctor hopes it was the latter. But for Lyra, seeing a friend cut down from the Cyberponies? That was hard. Brutal. He knew what it was like to lose someone, thanks to them. His mind drifted to a young colt from E-Space who had been like a son to him... to a prized golden star that saved his life then...but he couldn’t save the one who owned it...

Now tears were threatening to leave The Doctor’s eyes. His next focus was on former Elements of Harmony, who looked utterly broken. They had their entire world destroyed with everything they had been doing not only revealed to be wrong but manipulated by a greater evil than they could not have foreseen. The sight of their beloved Princess Celestia used as a tool for their destruction, and the end of Spike The Dragon, Princess Cadence, and maybe Princess Twilight had destroyed something in them that they would never regain.

This was just the typical actions of the Black Guardian, who used everyone and anything to get his way. In some ways, The Black Guardian reminded The Doctor of The Master, but he was more powerful due to his ability to warp reality in multiple ways. The only saving grace there was about him was that the Black Guardian consistently underestimated him with his arrogance, and the White Guardian always kept his powers limited due to his existence. He even recalled what the White Guardian said to him the last time they spoke:

“Be vigilant, Doctor. Once, you denied him the Key to Time. Now, you have thwarted him again. He will be waiting for the third encounter, and his power does not diminish.”

Now, that third encounter has come, many regenerations later. A part of him felt foolish for not realizing that the Black Guardian was behind this, but The Doctor also realized there was no knowing of the situation ahead of time. Maybe some things could have been prevented or done differently to stop so much death, but now was not the time to think of such things. Now was the time to take action and prevent the situation from worsening.

"Doctor," Lyra asked as everyone turned to her and she asked. "What...what is going on? All of this...what is this Black Guardian that...has used us like this."

"And those varmints that attacked us," Applejack asked in a cold yet sorrowful tone.

The Doctor sighed and shook his head. "Enemies of mine that I have faced before in the past. They have tried to destroy Equus before, and I've stopped them, but it seems they've gone further than I ever dreamed."

Everyone was now focused on him.

"The Black Guardian is the personification of all evil and chaos in the universe. Not the kind of chaos that Discord represents, but the destructive and death-dealing kind. In many ways, he is among the first and oldest of gods that exist in our universe, along with his brother, The White Guardian, who represents all things good and orderly. The Black Guardian has tried to become more powerful to rule or destroy the universe a few times, and I was tasked to stop him each time," The Doctor explained as he thought about his adventures searching for the Keys of Time with Romana and K9 as well as the Enlightenment incident with Turlough and Teagan.

"And the other two?" Dinky asked.

“The Daleks and Cyberponies. Two of the most evil races in the galaxy. The former was once called the Kaleds and lived on the planet Skaro. At least originally. They mutated during a war with their enemies, the Thrals, thanks to the scientist Davros, who accelerated the mutation. He put them in war machines and made sure that they only had one purpose in their entire lives: The destruction of all non-Dalek life in the galaxy. They are ruthless, feel no pity, and desire nothing more than the death of all living things besides themselves, which they see as inferior."

"...They destroyed my homeworld," Discord said, getting their attention as he closed his eyes. "My friends. My family. Everything was gone because of them. And I'm not the only one. Thousands of races have been wiped out because of them."

"...But why?" Fluttershy asked in complete disbelief over the existence of such evil.

"Because that's their mindset," The Doctor muttered as he began to type into the console. "As for the Cyberponies, they're your race's cousins."

"Cousins?" Dash asked in confusion.

"Equus had a twin planet known as Mondas that was knocked out of solar orbit and drifted into deep space. The Mondasians, already far advanced in technology and fearful for their race's survival, replaced most of their bodies with cybernetic parts and became known as the Cyberponies. Having eventually removed all emotion from their brains for pure logic, they soon realized they lacked the means to reproduce. They started invading worlds to convert other races into Cyberponies like them. Though there are various versions of the Cyberponies all over the universe, including one from an alternate dimension, they all share the same goal. Turn all life into cyborgs like them or, failing that, eliminate it."

"So they're just like the Daleks," Carrot Top said with a snort. "I bet they get along great."

"Actually, they hate each other and have been at war many times," The Doctor said with a snort. "I even was in a few of those battles."

"So why are they working together?" Lyra asked in confusion.

"No doubt that the Black Guardian is forcing or brainwashing them to do so," The Doctor said grimly. "He's powerful enough to do so. Much as the Daleks and Cyberponies like to think they are as powerful as they believe there are things more dangerous than them."

"...So how do we beat him?" Rarity asked with disbelief. "How...how can we just...beat such a thing? Princess Celestia is being controlled by him. Princess Cadence is dead. Twilight might be, as well. With her and Pinkie Pie dead, we can't use the Elements of Harmony. And Discord's magic won't work because of the Daleks. How...How can we win?"

"...There is only one possible way," The Doctor said with a heavy sigh as he began to type in coordinates. "We have to get humanity and Equestria to work together."

"Work together?" Carrot Top asked in surprise. "Doc, I hate to break it to you, but you have very little chance of that happening. Especially after what happened with the Harmony Cannon."

"Maybe if we explain everything-" Fluttershy was cut off by Flash Sentry.

"Yeah, let's tell the United Nations and every single human that Equestria is sorry that it's killed nearly a billion or so people because we got tricked by an outer dimensional god-like being of evil that brainwashed our leader into thinking the sun was going to die and kill us all," Flash Sentry said while rolling his eyes. "I doubt anyone is going to believe us, and even if they did, too many humans hate Equestria for the crimes it's done."

"Not to mention trying to convince Equestria is just as unlikely," Rainbow Dash sighed. "With half of the nation at war with the other half and that one half being zealots towards Princess Celestia who think that the humans are all evil, it will take forever to convince them."

"There is still Princess Luna," Dinky pointed out. "If we find her, maybe we can get her to lead Equestria? I mean... she's really the only Princess left that can lead it."

"And yet she's still not as popular or influential as most Equestrians save for those in the military," Flash Sentry said. "Princess Celestia was a goddess to so many. The fact that not only is that a lie going to break them, but her being controlled by a creature far more powerful than even Discord is going to make them shatter their minds."

"Well, we're going to need everypony we're going to survive this!" Lyra pointed out. "Because if we're not going to fight for our survival, we might as well just slit our own throats!"

"Everyone! Please!" The Doctor said, getting their attention. Sighing, he looked at them all. "Look, right now. We don't have a lot of time. The Black Guardian will strike, and if we do not do something soon, we will have a worse situation on our hooves. Here is what I propose. Discord? Do you have enough power to teleport you and a few others?"

"In a few minutes, sure," Discord answered.

"Good. Take Rainbow Dash, Rarity, Applejack, and Fluttershy to find Princess Luna and explain the situation to her. We will return to Geneva and explain the situation to Major-General Marshall Highmoor. He, at the very least, trusts me and can make it clear to the rest of the U.N. that the war against Equestria needs to end and, instead, they must work with them to face a new enemy. One more dangerous than anything their race has faced before. Right now, working together and ending this war must happen before we stop the Black Guardian. Not just because it's all pointless after everything we learned, but if the Black Guardian is doing what he says he is doing, the war is only fueling his ritual to bring himself into this dimension."

"What's going to happen if he succeeds?" Derpy asks with worry.

"End of all life on this planet as we know it. Human and Equestrian," The Doctor answered with a heavy sigh.

+}{+

Princess Luna had been prepared for everything to start her rebellion. She had gathered her forces to the south and made sure to only take the ones that would be absolutely loyal to her when she made her coup. She also established a base in the Macintosh Mountains using a base she remembered was part of a failsafe system crafted by the E.S.S. if Equestria lost the war. It held not only a strong defense point but also the most advanced technology and magical means Equestria had, along with a base big enough to keep her elite troops and personal guard. Once that was done, Luna sent envoys to the various rebellious forces, offering her support to them with promises to not only end the war and begin peace talks with the humans but also establish a constitutional monarchy in place of the absolute one they had. This was their request as they wanted to develop some form of new government where their non-elite had some power and could prevent tyrants from establishing themselves again. Although not a fan of democracy herself, Luna could see that they had a point, seeing as her sister was all but becoming a tyrant.

Princess Luna had been preparing a war plan with her officers when a guard told them that not only had Discord arrived with a white flag but also Rainbow Dash, Rarity, and Applejack, who looked like they had been through a warzone. What followed was a conversation that made Luna drink straight from a bottle of her hardest liquor because, in the manner of two hours, everything she had known about anything had changed.

The war was a lie.

All of it was manipulated by some dark god-like being who not only had taken possession of her sister but also brought genocidal aliens who had already killed Princess Cadence, Spike, and maybe even Twilight Sparkle. Ones that were not only more advanced than both humanity and Equestria but had wiped out entire worlds. It was taking all of Princess Luna's willpower to either not cry in tears of hysteria over the insanity that had become of her life or just scream to the heavens at whatever higher power there was that was bucking her in the flank. Not just because she and all of Equestria had been used like a whore by some alien god of evil for an unjust and dishonorable war that left millions of innocent people, ponies, and other creatures dead, but also for her sister. Her sweet sister had been manipulated and was now being worn by his foul demon like a skin suit.

"...Is my sister dead?" Princess Luna asked as she lowered her third bottle and slammed it on the table of her war room.

The three ponies looked at each other with worry and sorrow as Discord answered for them. "The Doctor believes that she's not technically dead, but it's unlikely she can be free without any harm to her."

"Meaning she's dead either way," Luna grumbled as she lowered her head. It was taking all her willpower to not sob for her sister's fate, but in the end, she was drawing on rage to keep her sanity. "This Black Guardian will feel my wrath before I take his head. Not just for Celestia but everyone else it has used and murdered in its sick and twisted game to become an all-powerful being in this universe."

"Ah'm surprised ya believe us," Applejack pointed out since it was an absurd story.

"You are not known to be liars, especially you, fair Applejack," Princess Luna pointed out while rubbing her eyes. "Besides, in the strangest of ways, this all makes sense. The reason why we are here, my sister's attitude, and so much more. Never before have I felt such rage and shame in my life. Not even as Nightmare Moon compares to this."

"The Doctor says that we need to work with the humans if we're going to defeat the Black Guardian, Daleks, and Cyberponies," Discord explained. "He said that only by working together do both sides have a chance to survive. Because if the Black Guardian wins, both sides will be wiped out."

"Done," Princess Luna said in an instant.

"Woah, that was just as fast as me," Rainbow Dash said with wide eyes.

"What choice do I have?" Luna said with a snort. "I am up against forces I cannot comprehend, and I'm the sole ruler of a broken nation that can collapse at any time. At this point, I'll even ally with Queen Chrysalis, Tirek, and Sombra if it means we survive. Tell The Doctor I agree to work with the humans. No doubt that they will want demands because of the war, and we can negotiate on that, but I agree that we have to work together."

"Do you think it will be just as easy with the humans at Geneva?" Rainbow Dash asked.

"Considerin' what humanity has lost and that they are a stubborn race? Probably not," Applejack sighed as nopony could disagree with her. "But if anyone can get them to work with us, it's him. He's already pulled a bunch of fancy tricks. Maybe he'll pull another one?"

Suddenly, a pale-faced purple pony in royal night armor burst in and shouted something that made them all freeze. "You're majesty! The Crystal Empire and Canterlot are being invaded!"

"Humans?" Princess Luna asked with an almost hopeful tone.

"N-No! From the sounds of it...and I can't believe I am saying this...but aliens!"

Discord closed his eyes and growled. "It has begun..."

+}{+

"Let me get this straight," Major-General Highmore said as he paced around his office with The Doctor and his companions inside. "You mean to tell me that Princess Celestia, the world's most wanted war criminal who is guilty of murdering over a billion human lives and who knows what else, was being mind controlled by this Black Guardian."

"Yes," The Doctor said as he went to talk, but Major-General Highmoore stopped him.

"And," He said with a heavy sigh. "This Black Guardian is the real manipulator and is seeking to come into our world by committing mass war and death on both sides."

"Correct," The Doctor answered.

"And he's also recruited two alien species from your dimension, which sounds like a bunch of pepper-potted Nazis and walking tinmen Communists who have wiped out entire planets."

"Affirmative," The Doctor sighed as he rolled his eyes.

"And," The Major-General put his hands on his waist and looked the Doctor straight in the eye. "You want us to team up with Equestria, the ones attempting to kill us all or convert us into ponies. Team up and defeat them."

"I'm guessing you don't believe me," The Doctor grumbled.

"Doc, much as I like you, and much as I want to believe you, there is no what in God's holy name am I going to try and convince the U.N, much less the military and the entire human race, to suddenly become buddies with the people who were attempting to exterminate us!"

"Funny he says that when the Daleks are the ones who do the exterminating," Depry whispered to Carrot Top.

"Not the time, Derpy," Carrot Top replied.

"Look, Major-General," The Doctor said, stepping forward. "I understand I am asking for much, and I know that this is something none of you wish to hear, but the Equestrians are also victims of this. They were tricked into leaving their homeworld, killing all life there, and being manipulated into causing a war that has also led them to suffer. I know you have suffered more, but this entire suffering is all because of the Black Guardian. And if neither of you works together to stop him, then he's going to wipe out both your races and rule this galaxy in a state of eternal darkness."

"If we can handle this war against the Equestrians, surely we can defeat this Black Guardian and all his allies," The Major-General said with a snort.

"No, you can't. Not alone," The Doctor said as he stared into the Major-General's face, and their eyes met. The Major-General then saw something that made him sweat. A combination of both fear and anger, as well as the sight of a person who has seen more bloodshed and destruction than humanly thought possible. "The Daleks and Cyberponies have no mercy, pity, or sympathy. They cannot be talked to, they cannot be negotiated with, and they don't even care how old or young you are. To them, you are nothing but an inferior insect that must be eliminated. They care only about one thing. The complete domination of their species over all others. Entire systems have fallen and burned because of them. They've started wars that have lasted hundreds of years and have filled entire plants of graves. Even the destruction of their own homeworlds doesn't stop them. And combined with the Black Guardian, who can be considered equal to your world's Satan, they will reign death and destruction that you cannot comprehend."

"...A billion lives are dead because of Equestria," Highmoore pointed out.

"All lives will die because of The Black Guardian," The Doctor replied.

Things were quiet between the two until the phone rang. Sighing, Highmoore pressed the speaker button. "What?"

"SIR! UNKNOWN AIRCRAFT JUST APPEAR ON RADAR! THEY'RE IN GENEVA! WE-"

Suddenly, there was an explosion, and everyone was knocked back.

+}{+

“Leader. Our Cyberships have begun their assault.”

“Excellent. Begin the invasion. Unleash the Cyber Forces.”

“Objective?”

“Capture all humans for Cyberconversion. Kill all who resist.”

“Affirmative. What of the Doctor and his companions?”

“Eliminate them.”

Author's Note

Not a long chapter. Figured we needed a bit of a small one before we see the Daleks and Cyberponies go to work.

As always, please help out at the NegotationsVerse TV Tropes Page: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 16

“Yeah, but that's it! That's exactly the point! Oh, Lumic, you're a clever man. I'd call you a genius, except I'm in the room. But everything you've invented, you did to fight your sickness. And that's brilliant. That is so human. But once you get rid of sickness and mortality, then what's there to strive for, eh? The Cybermen won't advance, you'll just stop! You'll stay like this forever. A metal Earth with metal men and metal thoughts, lacking the one thing that makes this planet so alive: people! Ordinary, stupid, brilliant people!”

-The Tenth Doctor

“You — are — my — enemy — and I am yours! You are everything I despise. The worst thing in all creation. I've defeated you. Time and time again, I've defeated you. I sent you back into the Void. I saved the whole of reality from you. I am the Doctor, and you are the Daleks!”

-The Eleventh Doctor

+}{+

It was chaos all over the world. They came from out of nowhere, and in an instant, many areas in both the human and Equestrian lands were under attack by forces beyond their beliefs. One was a racial purity-driven hateful race of exterminators who had only one objective in life, and that was the complete domination of the Dalek race over all others. They were ruthless in their killings of both humans and ponies. None were spared, not even children. Cities were in flames as many ran in terror or cried out for their gods to save them, only to emit one final scream before being silenced forever and joining those gods in death.

The other was a silver army of emotionless, logic-driven abominations that could no longer be called ponies. They were like a virus, immune to most weapons, with nothing in either human or pony hands/hooves that could harm them. While they did eliminate those who stood in their way, they had more sinister purposes for those they spared. Those taken from them would be subjected to horrible treatments that would see them lose their skin, flesh, and bones before becoming the very things that captured them in the first place against their will.

The world soon learned of these events. Fear and panic spread, and a desperate cry was called out.

“Someone save us.”

And someone was coming.

+}{+

The first thing The Doctor did upon waking up was make sure he hadn't regenerated again. It would be embarrassing if he did not long after being in this body. Thankfully, the only thing he was suffering from was a nasty bump on the head and a twitch in his rump. Moaning, The Doctor pushed the debris off his body and coughed up some dirt before looking around. The Major-General's room was utterly totaled, and there was a massive hole in the wall, showing the Doctor what he feared was most happening before his eyes.

Three large cyber warships floated above the city of Geneva, with their armies spreading across the streets. He could hear the battle already raging across the city, with the cries of many in terror or pain. Despite being a heavily fortified city thanks to being the HQ of the United Nations, The Doctor knew that none of the weaponry here would be able to fight off the Cyberponies.

He then looked around and saw that everyone else was thankfully alive and struggling to get up. It didn't take them long to see the destruction going on outside. Major-General Highmore ran to his phone and picked it up. "Report! Now!"

"Sir! We're under attack by what look to be robot ponies! All forces on all city fronts are doing their best, but our weapons are doing nothing! I swear this is like something out of Battlestar Galactica!"

"Is it just us or-"

"No! We got reports that Berlin, Islamabad, Algiers, Chicago, and Kwangju are also being attacked! Not just by these things but by...pepper potted...aliens that shoot lasers that instantly kill you?!"

"Daleks..." The Doctor hissed as Major-General Highmore looked at him before returning to his call.

"What about the civilians?! And the UN Council?!" Major-General Highmore demanded.

"The council has gone dark! We can't contact anyone inside! We're doing what we can to keep the population safe, but they keep taking civilians alive! We got reports that they're taking them into some transport ships and taking them to the bigger ones!"

"Cyber conversion," The Doctor answered as Highmore looked at him. "They're going to convert them into cyberborgs like them. Those people are already dead."

"...Any chance of reversing it?" Highmoore asked.

"No," The Doctor said, shaking his head. "Not even I can do that."

"...I want all forces to hold out as much as possible! Use every weapon we have! Even the classified ones! Get reinforcements at once! And I want birds in the air to wipe those ships out as soon as possible!" Major-General Highmore demanded before hanging up the phone. He rushed over to his desk, opened a drawer, and pulled out a bottle of whisky he drank straight up before slamming it down. "First ponies, then cyborgs. What's next? The Loch Ness Monster?"

"Major-General, none of your forces are going to do anything to the Cyberponies," The Doctor said seriously as he approached him. "They are beyond your technology. Practically any mundane weapon is ignored by their shields or armor. The best you can do is fire as many explosions and anti-tank weapons at them as you can, but at best, it will show them down."

"Then what the bloody hell do you suggest?!" Major-General Highmore demanded with desperation in his eyes. "If you have an idea, Doctor, say it! Because if Geneva falls, the entire U.N. will fall, and the world will fall into chaos!"

The Doctor bit his lip and looked outside, focusing on everything around him. The others looked at him with both hope and desperation. He had always had a plan for all the time they had been with him, and now, more than anything, did they need him. Lyra walked over to him and put a hoof on his shoulder. "Doctor?"

"...Lyra," He turned to her. "Stay with the Major-General. I'll deal with this."

"Not alone, you're not," Lyra said with determination.

"Lyra, this is serious," The Doctor said as he glared at her. "The Cyberponies are no laughing matter. Neither are the Daleks or the Black Guardian. This isn't just trying to stop a war anymore. This is trying to stop the end of reality as we know it."

"Then we'll stop it together," Lyra said as she poked him in the chest. "It doesn't matter if it's against Princess Celestia or this Black Guardian. I made a promise that I was going to end this war and bring peace to ponies and humans. If that means going to hell with you, Doctor, then I'm ready to dive right in."

"Us too," Flash Sentry said as everyone nodded.

The Doctor looked at them all one by one before sighing. "Ponies. Always a stubborn species." He then smiled. "But a courageous one as well."

"So what's the plan, Doctor?" Dinky asked.

"...I have an idea, but it's risky." The Doctor sighed as he turned to Major-General Highmore. "We need the Large Hadron Collider just outside the city."

"What for?" Major-General Highmore said in confusion.

"We're going to make it into a weapon," The Doctor said as he turned back outside. "If we can get to the TARDIS and get to it, there is a chance to save everything."

"But we parked the TARDIS blocks from here," Carrot Top moaned. "Why did we do that?!"

"Worry about my parking skills later," The Doctor said as he pulled out his Sonic Screwdriver. "Major-General, do what you can to slow the Cyberponies down! Get the civilians to bunkers, including Princess Flurry Heart! We'll do what we can!"

"...Guess I got no choice," Major-General Highmore said before saluting him. "Good luck, Doctor."

"We're going to need it," The Doctor told the man before turning to his team. "Right, let's move! Tally ho!"

+}{+

Princess Luna knew that becoming a princess meant you had to make tough choices in life. Every decision could mean the lives or deaths of hundreds or more. Today, she had to make a choice that would decide the fate of two cities.

Both Canerlot and the Crystal Empire were under attack by alien forces beyond their power, forces responsible for the deaths of all the other alicorns save for her and Flurry Heart. From what the others had described, their magic was all but pointless to use against the creatures whose purpose was only the genocide of all others. Meaning they were practically demons in metal armor.

Princess Luna knew she had to make a decision to save one of the two. The problem was she didn't know which one. Canterlot was the capital of the nation. The very heart and soul of the government. It was where their center of government, religion, and culture resided. If it fell, it would cause such a moral loss that the spirit of Equestria would be broken. On the other hoof, the Empire was a valuable resource area. The crystals it housed made up much of their magical properties and technology. It also was the only city that housed the Crystal Ponies. If it fell, they would be wiped out. An entire race could be erased from existence. Yet, wasn't her loyalty to the actual Equestrians first?

"Going up against the Daleks is suicide," Discord said to her. "Few races can stand up to them; if my people couldn't, I doubt you can."

"I am not foalish, Discord," Princess Luna said as she glared at him. "My concern is to free my subjects and save as many lives as I can. Not fight an enemy I cannot defeat on my own."

"So, what? We're just going to sit on our tails and do nothing?" Rainbow Dash demanded.

"...No, I have an idea of what to do," Princess Luna sighed heavily. "My sister and I prepared a backup plan in case Canterlot was ever in danger—a means to save it. However, it required the power of two alicorns to use. With no other alicorns, I am afraid I cannot use it."

"Ahem?" Discord raised his eyebrow before snapping his fingers as a dozen neon light signs pointed at him. "I might not be an alicorn, but I have greater power than that. Surely I could be of assistance?"

"...Yes, that would work," Luna said with a nod. "We will need to get to the palace. I can only pray it is not too late."

"What about the Crystal Empire?" Fluttershy asked as all eyes turned to them.

"...I will accept full responsibility for their fate," Princess Luna muttered.

"You're going to abandon them?!" Rarity shouted in shock.

"What choice do I have?!" Luna shouted, which surprised them. She calmed down and explained. "I only have enough forces to save one city. And I have no means to rescue the Crystal Empire. Not even for a mass teleportation escape. This is war and survival. I will answer for their deaths in whatever Hell exists in this cursed universe. Please say if you have any other ideas that could change my mindset."

Nobody said anything.

"...Will you be joining us, or will you sit this one out?" Luna asked.

"...I think I need a moment after everything that's happened," Rarity whispered as she slowly sulked off. Fluttershy gave an apologetic look before following the unicorn.

"And you two?" Princess Luna asked the remaining Elements.

"I'm not about to back down now," Rainbow Dash answered.

"Same here," Applejack replied as she lowered her hat.

"Then let us be off and pray that fate is not against us," Luna said.

+}{+

When Flash joined the Royal Guard, he knew there would be times when one had to stomach the sight of death and destruction. He thought he was ready, especially when the war against humanity began, and he switched sides to join the Underground Railroad. He had been in battle before, but this one was different. This was a one-sided slaughter as it was clear that the Cyberponies held all the advantages. From what the Doctor had explained, they were not only scientifically advanced but also developed a means to adapt to any weaknesses they fell victim to over time. The only strategy was to run.

The TARDIS was a distance away, near a museum that they parked next to, but they needed to go through the streets themselves to get to it. At first, this wasn't a problem; they ran or flew as fast as possible to get from one street to another. Civilians were running around in a panic, guided by soldiers making fortifications for when the lines further up fell. And from what they could tell, they were falling fast.

They had to cut through alleys and a few abandoned houses to keep going. The Doctor led them all the way while his Sonic Screwdriver remained out, scanning every so often. Flash decided to ask the question everyone was thinking: "So what is this Hadron Collider thing, and how is it going to help us against the Cyberponies?"

"Basically, it provides collisions between lead ions, recreating conditions similar to those just after the Big Bang. When heavy ions collide at high energies, they form for an instant the quark-gluon plasma, a "fireball" of hot and dense matter," The Doctor explained." While humans have been using it to test different theories of particle physics, I can use it for something else."

"Like what?" Dinky asked.

"Well, it wouldn't be much of a surprise if I told you, did I?" The Doctor said with a quick smile before he opened the door to a bakery across the museum. The problem was that they were facing the other side of the museum, not the one where the TARDIS was located.

"Right, so we just need to get to the other side of the museum. Get in the TARDIS. And we're safe," The Doctor said to his team with a small smile. "Simple, right?"

"When has anything with you ever been simple?" Lyra pointed out.

"True," He admitted with a shrug. "But maybe this might be the first."

"Well, let's go!" Derpy said while finishing one of the muffins she had taken as a snack from the bakery.

They started heading for the museum, and things were fine at first...

...until a laser blast echoed in their ears, causing them all to duck as a car exploded not far from them. Looking to their right in fear, they saw a squad of Cyberponies heading their way with weapons drawn.

"Inside, now!" The Doctor shouted as everyone fled up the stairs. The Doctor used his Sonic Screwdriver to unlock the doors and get everyone inside before locking them. They wouldn't hold them off for long, but anything that gave them a few seconds of survival was worth it.

"This way!" The Doctor shouted as he led the group into the museum.

A few seconds later, the museum doors were blown open, and the squad of Cyberponies marched inside. Scanning the area, they tried to see where their targets were but found no trace of them.

"Spread out. Find the Doctor and his companions. Eliminate them," One ordered.

"Affirmative," The others said as they proceeded to walk in various directions.

+}{+

In Canterlot, many felt it was the end of the world. Never before, in the history of its existence, had it ever faced such a destructive threat. The moment the invasion began, it was bombarded by the alien spacecraft that saw hundreds dead in the first few minutes before ground forces arrived. The Daleks, screaming their catchphrase, started wiping out all non-Dalek life around them as was routine.

The ponies of Canterlot scattered as they fell one by one to the death rays. Screams of the agonized deaths from their fellow ponies were some of the last things they would hear before being killed themselves. There was no sparing of anyone. No matter how much they pleaded, prayed, begged, or even bribed, they were killed without mercy. Even the tears of scared foals were nothing to sway the pitiless Daleks.

Canterlot's forces, Royal Guard, Police, and Military, acted as quickly as they could, but it soon became apparent that they were dealing with something just as bad, if not worse, than humanity. The Daleks were not harmed no matter what weapons or magic were used. Their energy shields bounced any feeble attack before firing back and taking down the soldiers individually. The best they could do was produce shields that could protect them, but these would only last so long before they were shattered and their forces overwhelmed.

Captains had to make tough choices, and some were forced to put shields between them and retreating civilians. The soldiers had to watch in horror as the citizens, begging to be saved and banging on the shields, were wiped out by the Daleks, who cut through them without mercy before firing on the shields. Orders for reinforcements were sent. Many wondered where Princess Celestia and the other Alicorns or even the Elements of Harmony were? Some sought refuge in the grand cathedral dedicated to the alicorns, their goddess. Many prayed for their deities to come down and save them, but when the Daleks burst through the glass windows and fired upon them, there was soon nothing but the silence of a dead faith.

The moment Princess Luna's forces arrived at Canterlot Palace, their hearts sank at the destruction they saw: burning buildings, streets torn apart, icons and wonders shattered, and the smell of death as bodies lay motionless all over. After collecting herself, Princess Luna ordered her forces to reinforce any location with their magic and weapons. The palace was currently the most under attack, and it couldn't fall if they were going to get anyone out of this alive.

"I need a sitrep now!" Princess Luna demanded as she and her group marched forward through the halls.

"It's chaos, Your Majesty!" a Lieutenant of the Day Guards said as he walked forward with her. "We got reports of the invaders all over the city! Multiple casualties up to the thousands! Fires are everywhere! The palace is under attack from all directions, and we're losing ponies!"

"Whose in charge at the moment?!" Princess Luna demanded.

"Right now...I am," he said with a sigh. "Lieutenant Valorous at your service."

"The military leaders?"

"Dead," He said in despair. "The military HQ was one of the first places to be destroyed in the early bombardment."

"Damnit," Princess Luna grumbled.

"Your Majesty, where is Princess Celestia or Princess Twilight?" He asked.

"...Dead," Luna answered, which brought all ponies in the entire area who had heard this to a silent halt of horror. "My sister and Twilight are dead. As of now, I am in charge of all of Equestria."

"...B-B-But that's not possible! They were-”

"WE ARE NOT GODS!" Luna shouted with the Royal Canterlot voice. Everypony stared at her before she sighed. "We are not gods. We never were. I curse the day my sister let this stupid false faith exist. I am tired of the lies and deception. I will expose the truth of everything, but first, our priority is survival. I have a way to save us all, but I need the palace protected at all costs! Understood?!"

There were mutterings and nervous answers, but it was clear that everypony was shaken up by what was just said. Nevertheless, survival instincts and duty took precedence as everypony went to work. Concerned, Applejack walked over to Princess Luna. "You okay, Princess?"

"No, but my feelings are not of any concern at the moment," Princess Luna sighed as she rubbed her forehead. "I fear even if we escape this day that Equestria has fallen from the grace it once had...if there was any grace..."

A tear dropped down Luna's eye before she wiped it away and turned back to the others. "Right, saving Canterlot will take time, even with me and Discord. Fairest Applejack and Rainbow Dash, I hate to ask this of you, but Equestria needs you again. Will you fight beside our comrades here and protect the palace? With your lives if necessary?"

Rainbow Dash and Applejack looked at each other and nodded, saying, "Always Princess."

"Yeah," Rainbow Dash flared out her wings and grinned. "Let's kick evil butt like the old days."

And this time? It would be for the right cause.

+}{+

The Doctor, Lyra, and Flash Sentry were together and running through the halls of ancient Earth civilizations in a desperate attempt to keep themselves as far away from the Cyberponies as possible. The two ducked behind a corner leading to the Mesopotamia section and took a moment to collect their breaths.

"Okay, when you said there was a lot of running when it came to being your companion? I didn't think you meant this much running," Lyra grumbled.

"I did warn you," The Doctor said with a nervous smile.

"Come on, Doctor. There has to be something we can use on these tinheads!" Flash Sentry asked in desperation.

"Nothing I can see at the moment," The Doctor sighed. "Conventional weapons will not work on the Cyberponies. Their armor and shields are too strong. If we could grab one of their weapons, we might stand a chance, but good luck trying to steal that from a living Cyberpony."

The speech was interrupted by a blast of the laser hitting the corner, and the three of them ran again. The Cyberpony appeared from around the corner, blasting as fast as possible while they ducked and used whatever priceless artifacts and displays could be used for cover. It was a shame, in a way, that these works of ancient art and smithy were destroyed in such an ungrateful manner, but for the three running for their lives, it was worth the cover.

Lyra turned around to see if the Cyberpony was on her tail, only to trip over a "Wet Floor" sign and fall onto her stomach. Groaning, Lyra looked up and saw the Cyberpony aiming its weapon at her. Her heart stopped upon seeing the barrel pointed right at her face. Flash, having seen what happened, gasped. "Lyra!"

Without thinking, he grabbed a nearby golden-made spear and flew forward as fast as his guard training kicked in. Shouting in rage, he shoved the spear right at the Cyberpony. What nopody, including the cybernetic abomination, had expected was for it to go right through the chest and cause sparks and a small explosion to erupt. The Cyberpony screamed in a synthetic voice of pain and agony as it backed away, shaking before falling down lifeless.

Flash and Lyra looked at the motionless creature in shock, the spear still in its chest, as they both looked at it. The Doctor rushed up beside them and stared at the Cyberpony in disbelief. "You...You...You killed it!"

"Uh, yeah," Flash Sentry said as he floated down and helped Lyra up. "I did."

"How?!" The Doctor said in disbelief as he pulled the spear out. "How could a spear have killed a Cyberpony?! Even if it's made of gold, it shouldn't have worked!"

"What does being made out of gold have to do with anything?" Lyra asked.

"Well, for the longest time, gold was the weakness of the Cyberponies, but they found a way around that. So how could it have killed..." The Doctor's eyes widened. "Unless..."

He took his Sonic Screwdriver out and scanned the spear before looking at it. A look of joy appeared on his face. "Oh, that's just fantastic!"

"What is it?" Lyra asked.

"It's a different chemical formula! A different chemical structure! Even a different atomic structure! Of course, different dimensions! Even if it looks and feels the same, it doesn't mean it's the same down to the same atom!" The Doctor said with glee. "The Cyberponies might have immunity to our dimensions' standard of gold, but not this one! One we can use to fight back!"

"Hey!" They turned around to see Derpy, Dinky, and Carrot Top running over to them. They paused when they saw the dead Cyberpony. Derpy walked over and knocked it on the head. "Um, I think it's dead."

"Very much dead! And thanks to Flash Sentry here, we have the means to make sure we can make any Cyberpony meet the same fate," The Doctor said as he tossed the spear to Flash Sentry. "Everyone grab a golden weapon! Time to show the Cyberponies that the classic way of warfare still has merit in this day and age!"

Author's Note

Yeah, it's been awhile hasn't it? After holidays I went to card dealing class for the casino I work at which made my super busy and afterwards I was adjusting to so much and dealing with stuff. Kinda still am but I never forgot this story.

We're back.

As always, please help out at the NegotationsVerse TV Tropes Page: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 17

“There are some corners of the universe which have bred the most terrible things! Things which act against everything we believe in. They must be fought!”

-The Second Doctor

“I reversed the polarity of the neutron flow.”

-The Third Doctor

+}{+

When Private Jolt Bolt discovered his talent for shooting electrical currents from his horn, he could have done several options with his talent, from charging up stuff to working on electrical plants to even having a job in the Lighting Storm department of Cloudsdale's Weather Factory. However, when it was clear that war against humanity would happen, he quickly joined the Royal Guard to serve his country. Jolt Bolt wouldn't say he was like many of the various human haters out there, but he did believe in his country and in protecting it. However, with everything that had happened, especially with the Harmony Canon, he wondered if he was on the right side.

All the things he was taught about Harmony and Friendship growing up? What they were doing wasn't it. Even his area of Equestria had decided it had enough and declared secession from the country with letters from his friends and relatives urging him to get out of Canterlot and come home. Jolt Bolt had thought about it long and hard. He loved the Guard. There was a brotherhood to this order, and he took an oath to protect Equestria. But what part of Equestria was he supposed to protect? The side he agreed with or the side that he was sworn to serve?

It didn't matter because he only needed to focus on one objective: protecting Canterlot and its citizens. Not from humans, but these things were worse than any of them could imagine. The Daleks (They practically announced themselves as such) were ruthless and held no mercy. They were shooting lasers of death at anything that moved. Ponies were shot without any hesitation. Entire streets were filled with corpses that held twisted faces of agony, showing their deaths had been anything but pleasant.

Jolt Bolt had thrown up more than once, and he was sure he would never be the same again. Some of his own fellow soldiers had fled in terror, screaming in fear. Others just rushed forward in suicide charges with grief and anger. The same ones kept doing what they could with their magic. Holding shield after shield and firing spell after spell. Even ones designed only for emergency uses were used that saw entire buildings and areas covered in fire and devastation.

But barely anything worked. Only the most powerful and biggest spells did some damage. The enemies took very few casualties. But for every Dalek they defeated, they lost ten of their own. The shield spells held off for about ten or twenty minutes at best before being destroyed and forcing them to take more casualties before building a new line. Unicorns were worked around the clock to exhaustion as "Pepper Up Potions" and "Magicka Potions" were given to help them keep going. Even illegal substances were allowed in this crisis.

When word came that Princess Luna had arrived with the Elements of Harmony, there was hope they could come out of this alive. They were all told to hold the line. Hold the damn line.

"I never thought I'd say this, but I wish I was fighting the humans again," Private Amber Wave said as she drank her third "Pepper Up" potion in the last hour. She was part of the squad that Bolt was with. It's not his original squad. They all died in the first ten minutes of the invasion. Anyone who lost their team was quickly assigned to whoever needed more ponies. He was sure everyone in his group was the sole survivor of their own squad.

"What are these things? Demons?" A pegasus Guard asked in terror. "What do they want from us?"

"Haven't you been hearing the "Extermination" stuff they've been sprouting every five bucking seconds," A rugged brown Earth Pony growled. "They're here to kill us all! All of us! This isn't a fucking battle! It's a slaughter! We're getting our flanks owned, and nothing is stopping them!"

"The goddesses will save us. Princess Luna is here," One nervous unicorn whispered as she hugged her sun pendant. "Surely the others will be here soon to save us like Princess Celestia?!"

"Oh, quit with the religious spiel," The rugged Earth Pony spat. "If the so-called goddesses were divine, we'd be saved already. This war with the humans would have been over long ago. Face it. They're just like us. Flesh and bucking blood."

"This has to be our punishment," One other Earth Pony moaned.

"For what?" Private Amber Wave asked in confusion.

"Everything. The attacks on humanity. The Conversion Potion. Declaring war on them. The Harmony Canon. This is the universe telling us that we've made mistakes and are reaping what we sowed."

"...Even if that's true, we can't just give up," Private Jolt Bolt said with a heavy sigh. "If these things are determined to kill us all, then we have only one option. We fight. And pray that whatever Princess Luna is doing will see us safe."

"...They shot a baby."

Everyone went quiet as they slowly turned to a pale pegasus pony staring at the corner with his eyes void of any life in them. "I saw them shoot a newborn as if it was a rat. It had to be no more than three weeks old. What...what kind of creature does that?"

Nopony answered

The door opened as one of the Guard officers, sweating like crazy, rushed inside and ordered them to return to the frontline. They all did, but the pegasus soldier was still staring at the corner. The Officer looked ready to yell at him, but Private Jolt Bolt stopped him and shook his head. The Officer paused to look at the broken guard, who seemed to be so zoned out that you could hit him with a rock, and he wouldn't move. Sighing, the Officer nodded as the two returned to the front line.

+}{+

"So, are you going to explain your plan to get all of Canterlot out of here?" Discord asked as he walked with the Lunar Princess down the halls to the throne room. "Because it's something I am inquisitive about."

"Let it not be said that my sister was not ill-prepared for events that I wish were not happening right now," Luna said as she made her way to the throne room. Using her magic, she pulled a hidden switch under the throne of the sun that caused it to slide to the right and reveal a secret passageway that led down a hidden level.

Motioning for Discord to follow, the two made their way down the dark steps, lightened by Luna's horn. They then came across a large double steel door with magical locks and curses that vanished as soon as Luna's magic flickered across the doors. They opened, revealing a small stone oval of a room with a single object on a stone platform. It was some kind of orb on a purple holder glowing with power.

"What is it?" Discord asked.

"It's a teleportation orb, but one that has the power to teleport the entire population of Canterlot," Luna sighed. "A last resort to save the people over the city itself. It locks onto the signature of every pony in the area and teleports them to wherever we wish, so long as it is in Equestria. This is what we will use to get us all to safety."

"Clever," Discord said before poking Princess Luna's behind, much to her annoyance. "I'm sensing a butt, however."

Rolling her eyes, Luna said, "It needs to be charged up. My sister and I were the only ones who could make it work, but with her...gone...I need you to help me charge it up. It will take longer since our magic differs, but I am confident we can make it work."

"Well then," Discord soon lifted his hands while sparking them with chaos energy. "Let's get started and get the heck out of there."

Luna nodded and charged her horn before the two sent their magic onto the glowing orb.

+}{+

Cyberpony Unit B031-8D031VS continued to scan the perimeter of the newest area in their search for their objective targets. The ponies seen entering this establishment had been identified as The Doctor and his companions. Making them priority one targets. Not one to underestimate their long-time adversary, the Cyberponies called for backup that would arrive in an estimated fifteen minutes. Until then, they were under orders to try and eliminate the ponies.

Cyberpony Unit B031-8D031VS made their way down a corridor when their sound sensors indicated noise. “HEY!”

As they turned, the Cyberpony Unit B031-8D031VS found themselves face to face with one of their targets, a yellow Earth Pony with a carrot Cutie Mark. The pony waved them over before tauntingly spanking their flank in their direction. “Come and get me you oversized tin soldier!”

Marching forward, Cyberpony Unit B031-8D031VS raised their weapon and fired as their target fled around the corner. Increasing the power of their limbs, they marched further onward and turned around the corner to see another one of them shove a spear towards them. It only took a second for their sensors to realize it was golden, but before they could do anything, the spear went through their chest.

For the first time since their conversion, the Cyberpony Unit B031-8D031VS let out a piercing scream of agony as their entire systems shut down. They collapsed to the floor, dying. In a desperate attempt to survive, the robotic self that had taken over their entire being struggled. But deep within, the equine part of them, long buried, finally breathed a sigh of relief.

The last of its life support systems died as Cyberpony Unit B031-8D031VS, formerly known as Kimbret from the Colony of Elitha on the Planet Emoria, embraced their demise with gratitude. At long last, they had been given what they had wanted for four hundred years.

Freedom.

+}{+

“Looks like it does work,” Flash Sentry said as he lowered the spear. Derpy was poking the dead Cyberpony before picking up its weapon. “At least we got a fighting chance now.”

“Right, no time to lose then,” The Doctor said as they took out their Sonic Screwdriver and pointed it at the Cyberpony before putting it away. “Let’s get out of here! We need to get to the TARDIS.”

The entire group nodded and ran or flew forward as fast as they could. There was not a lot of time left to spare and they needed to hurry. As they made their way to the large staircases that lead downwards, the group was fired upon by two more Cyberponies coming down from the other direction. Ducking from a blast, Dinky took her bow and arrow, armed with golden arrows, and fired one. It hit deadset in the chest of one of the Cyberponies who screamed, sparked, shivered, and fell down like a puppet without strings. The other Cyberpony didn’t even flinch or show concern, just continued to fire at the group.

They raced down, doing their best to avoid the blasts while the sound of more Cyberponies could be heard on the first floor coming to their location. Flash and Lyra, armed with their own golden weapons charged forward. The Cyberponies saw them coming and prepared to fire until the Doctor used his Sonic Screwdriver. He had accessed the Cyberponies systems as it was dying to grab some code and cook a little small virus of his own. The Cyberponies were, at the end of it all, machines who had to follow computer logic. While the entire Cybernetic Mainframe and System would take dozens of lifetimes to hack, that didn’t mean he could do a few small systems here and there. Such as weapons and sight.

The Cyberponies paused as their weapons suddenly shut off and their vision was blacked. Enough time for Flash Sentry and Lyra to attack them with their golden spear and swords respectively. The Cyberponies screamed and sparked as the weapons tore through their normally invincible armor and short circuited them leaving them to die in agonzing states before shutting down.

“I don’t suppose the Daleks will be just as easy to defeat like this?” Carrot Top asked The Doctor as they watched the slaughter from behind a statue with Dinky shooting arrows to support them. Meanwhile, Derpy was trying to figure out how this Cyberpony weapon she got worked.

“No, while the Daleks have a few weaknesses, they are technology more advanced and dangerous then the Cyberponies. Still, hopefully the others can find something to halt them,” The Doctor said.

“Hey, I think I got this work-” Derpy said before a blast fired upon the gun and headed straight to the second floor. The Cyberpony from earlier shooting at them had started to descend to ambush them when the blast blew up their head. Their motionless corpse collapsed and rolled down the stairs until it reached the bottom. “Oops. My bad.”

After stabbing the last Cyberpony, Flash looked at Lyra with an impressed look on his face. “Where did you learn to use a sword like that?”

“Bon-Bon...or Sweetie Drops I guess,” Lyra paused for a moment to look down in sorrow at the mention of her old friend, “said I should learn some kind of self-defense as a means of exercise. I didn’t think I needed to since Ponyville was practically crime free but I did it anyway since it worked well on my figure.”

“Yeah, I can see the result,” Flash Sentry whispered before blushing. “From the uh, way you killed the Cyberponies.”

“O-Oh, thanks,” Lyra blushed as the two looked at each other awkwardly.

“Ahem?” The Doctor said which caused the two to snap back to reality. “If we’re done here may I suggest we head back to the TARDIS?”

Nopony disagreed and they finally hurried to the back entrance where they soon found the TARDIS parked across the street and hurried towards it just as a new Cyberpony squad was advancing down the street. “Inside everyone!”

Once the door was closed, the TARDIS soon vanished just as the Cyberponies fired on it only to miss as it soon transported.

+}{+

Meanwhile, up in the main attack ship, The Cyber Leader was sitting on his captain's chair on the bridge as one of their Lieutenants walked over."Leader. Cyber Squad 2810-Delta-921 has reported. The Doctor and his companions have escaped."

"Unfortunate, but it does not change our plans."They said without looking at the other Cyberpony

"There is another thing. They have found the bodies of Cyber Squad 9193-Omega-264. They were destroyed."

That got its attention, and he turned to the messenger. "How is that possible?"

"Sensors indicated that they were killed with golden weaponry."

"Impossible. Our bodies have long been accustomed to our old weakness's...unless..." Their Advanced Logic Systems started working before coming to a conclusion.

"Unless, what? Leader?"

"Unless the gold of this dimension has different physical properties. Alert all units to be weary of any gold. We must seek to fix this weakness."The Cyber Leader said urgently.

"Affirmative."

"Very well. Continue the attack."The Cyber Leader said as it focused on watching the slaughter. Although some wondered where the Doctor was going or doing, he focused on his primary objective. What could The Time Pony do anyway to stop this?

+}{+

“EXTERMINATE!

Private Jolt Bolt was really starting to hate that word. He watched as another one of those death beams hit another soldier, who screamed in agony before falling down dead. The Daleks had practically taken half of the city by now, and there was no telling how many dead there were littering the streets. The good news was that all the civilians were behind their lines. The bad news was that, without civilians to fight, the Daleks focused on their soldiers and quickly lost numbers.

However, there was hope, and it came in the form of a Sonic Rainboom. There was practically a cheer from every corner in Equestria upon seeing the legendary move performed by the Element of Harmony, Rainbow Dash, who used it to blow away the Daleks and take out a few. The sonic wave had damaged their enemy, and they could breathe at last for the first time.

“ALERT! ALERT! UNKNOWN MAGIC FORCE HAS SHORT CIRCUITED SHIELD! ATTEMPTING TO RESTORE POWER TO DEFENSES!”

If there was one good thing about these Daleks, it was that they talked too much. Upon hearing that, every commander ordered their squads to get up and line up for a quick counterattack. Private Jolt Bolt was one of those who stood up on all fours, reinvigorated by the change of events. The order to charge was given, and he screamed in anger and fury along with the rest of the Royal Guard as they galloped forward. Out of the corner of his eyes, he saw that one mare without armor was charging with them. She wore a cowpony hat, and her yellow mane was breezing through the wind.

Applejack Apple. The Element of Honesty.

This only pushed Jolt Bolt to move faster.

Charging his horn, he let out electrical blasts at a Dalek who screamed about being attacked as a two Earth Pony tackled it off its surface while a pegasus from above fired crystal arrows at it from its crossbow. Jolt Bolt continued to blast it with electrical powers as the Dalek randomly fired its energy beams. One of them did manage to hit the pegasus and kill her, but this didn’t let up the others. Only increased their efforts to damage or destroy the damn thing. Finally, one of Jolt Bolt’s blasts went through a crack in the armor and shocked the Dalek inside. It screamed in agony before smoke emitted from the opening, and it went silent. The smell of fried...something was in the air, and that was enough for Jolt Bolt to assume it was dead.

He swiped the sweat from his face and saw that similar actions were being done on the Daleks as everypony used whatever skill they had to finally damage the bastards. There were still casualties, bodies falling as their skeletons were seen from the blow of the blast before joining their comrades in the afterlife. But it didn’t matter; they were finally on the offense.

He saw Rainbow Dash zipping around in the air, slamming her hooves into the Daleks with high, breakneck speeds that knocked them down. Applejack uses her powerful legs to do the same while using her rope to pull a Dalek back from attacking and allowing others to ambush it. Private Jolt Bolt snapped out of his admiration to finally get back into the fight. If he would die today, let it be in honorable combat with his comrades.

+}{+

Once the TARDIS landed in the operating room of the Large Hadron Collider, the Doctor went to work at once. The good news is that the staff evacuated when news of the alien invasion was reported worldwide, so nobody was there to stop them. Thanks to the Doctor’s Sonic Screwdriver, all doors were easily accessible. Once they reached the central power station, The Doctor got to work and used his Sonic Screwdriver to access all systems while correctly calculating his plan.

“So how is this going to help us exactly?” Lyra asked.

“The Large Hadron Collider is capable of creating various electromagnetic fields that the scientists here have only barely scratched the surface of. But since you’re talking to a member of the species that is one of the most brilliant races in the universe (well, our universe) this is all childs play to me,” The Doctor said, his confidence in his abilities shining through.

“So you can use one of those fields as a weapon against the Cyberponies?” Flash asked hopefully.

“Yes! All I have to do is put in the right equation, reverse the polarity of the neutron flow, get the system ready, and we’ll have a unique field that will simulate the actions of an EMP but only focus on the Cyberponies,” The Doctor said with a grin. “Good thing I got that code from our deceased friend from earlier. It's all falling into place, isn't it?”

Putting in the last number, the Doctor walked over to the button and took a deep breath. “Hang on to your flanks because here we go!”

He pushed the button, and in an instant, the Large Hadron Collider roared.

+}{+

“Leader!” One of the Cyberponies at the computers in the bridge of the primary warship. “We have detected a large unknown energy source traveling towards us fast!”

“What is it?!”The Cyber Leader demanded as the Cyberponies calculated.

“It’s a powerful EMP wave! Calculations state that our defenses are powerless against it!”

“Evasive maneuvers! All units are to-” The Cyber Leader didn’t get a chance to finish as the wave spread across the city. The ship began to spark and stutter as the EMP did its work. The Cyberponies were also affected as electrical currents shook out of their bodies, causing them to scream in digital ramblings as their entire systems started to fry. Their heads exploded one by one before the ship finally exploded and began to fall to its doom before crashing on the ground.

Similar effects were happening all over the city as ships, tanks, and Cyberponies themselves started to shut down in explosive means that saw their bodies blown across the streets. Humans looked on in awe as the silver robotic army, something out of a Terminator Movie, started to die in droves. When the last Cyberpony spoke its last garbled word and fell to the ground, dead, there was a sudden silence from the survivors.

Nobody cheered or laughed in victory.

All they could do was sit down and feel grateful that the nightmare was over.

+}{+

“When you said it needed a lot of power I didn’t think it was going to need this much!” Discord shouted as he struggled to maintain his focus. He even created a few extra limbs to wipe the sweat off his brow and give him a water bottle to drink.

“We’re almost there! Just a bit more!” Luna said as the castle began to rumble. “Shit, they must be attacking the palace! Hurry, Discord!”

+}{+

Private Jolt Bolt gasped as he struggled to deal with the pain in his head due to casting so many spells. He swore his head was about to split but had to keep going. He had to keep fighting. He was a Royal Guard. His duty was to protect the ponies of Equestria even until the end. He was about to prepare to attack another Dalek when each of them soon glowed blue and sent out a wave of energy that obliterated any nearby pony, including half of Jolt Bolt’s squad, to dust.

“SHIELDING RESTORED! COUNTER ATTACK! COUNTER ATTACK!”

Jolt Bolt cursed and started to run away, as did all others near the Daleks, who began firing at them rapidly. The screams of his comrades dying in droves were echoing in his ears as Jolt Bolt did his best to avoid the blast. Above, he saw the flying ships of the Daleks attacking the palace and trying to bring it down as its magical defenses began to falter.

He focused on running away until he heard a scream and saw a rainbow figure falling from the sky and crashing into some barrels nearby. Instalively, Jolt Bolt ran to the downed pony and saw that it was a wounded and dazed Rainbow Dash. He nearly gagged upon seeing the damage done to her right wing. It was practically burned off and crispy like a burned hayburger. You could see even the bone sticking out.

The Element of Loyalty was still alive but unconscious as he tried to get her up but soon saw a Dalek approaching them. “EXTERMINATE!”

The entire world seemed to slow down as the Dalek fired its shot. Jolt Bolt realized it was coming for Rainbow Dash. He slowly stood before it, the beam of death coming closer. Jolt Bolt saw his life flashing before his eyes from birth to now and held no regrets. He prepared himself for his end only to see him glowing a purple aura before there was a flash, and things went weird.

Colors swirled around him, and he felt like his body was thrown in different directions. He felt his body land on something soft and soon realized it was grass. Opening his eyes, he saw that he and those around him were no longer in Canterlot. They were in some kind of forest area near a large mountain.

The moaning of Rainbow Dash soon got his attention, and he helped her sit up. “What happened? Are we dead?”

“No,” Jolt Bolt sighed as he saw the clear and calm atmosphere. “We’re alive.”

They had survived.

But he had a feeling that it was only the beginning.

Author's Note

Hey guys, here is another update for you all! I'll try to get the next one out as soon as possible.

Please be sure to help out at the NegotationsVerse TV Tropes Page:https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 18

"Injustice is the rule, but I want justice. Suffering is the rule, but I want to end it. Despair accords with reality, but I insist on hope. I don't accept it because it is unacceptable."

-The Eighth Doctor

“I am and always will be the optimist. The hoper of far-flung hopes, and the dreamer of improbable dreams.”

-The Eleventh Doctor

+}{+

The aftermath of the invasion from the Cyberponies had all of Geneva in mourning. The list of dead was more than half the entire area's population. Combined with the knowledge that some of them had been taken away to be turned into "Cybermen," you had a population in complete despair. It was even worse, considering what had happened with Berlin, Islamabad, Algiers, Chicago, and Kwangju. Entire populations completely genocided to the last child or disappeared to be turned into metal monsters. The world was in a state of total fear and paranoia as riots and chaos happened all over. Some finally couldn't take it anymore. First ponies, then cyborgs, then alien nazi's. It was like sanity had collapsed, and the world's end was here. Various local and national governments collapsed or were forced into extreme measures to keep order.

Major-General Highmore felt like he was losing his sanity as he put a cigarette to his lips. He wasn't supposed to smoke on the job but damn the rules in this case. He had just gotten the worst report of it all. The U.N. council was gone. All the world's leaders or representatives were captured by the Cyberponies and taken away. Based on what the Doctor told him about cyberization, they were as good as dead. So far, the only people he knew were those he trusted, and the new leaders of each nation were coming into power to reestablish some form of order if they could.

There were mixed orders, chaos, and utter confusion in a world that had thought the Equestrians were terrible enough. Now, they had to deal with new threats. One of which, if the Doctor was telling the truth, was Satan incarnate. He could only hope the God version would come at this point.

The Doctor was doing what he did best, and that was healing what he could; all his companions were doing so. Major-General Highmore was too busy looking over everything from his room and needing a minute to gather himself. He looked at the ruins and wondered if this really was the twilight of mankind. After all these centuries of achievement, they were now dealing with a threat they couldn't deal with usually. Fighting each other now seemed pointless as nations were doing what they could for each other to the point that North Korea and South Korea had become united again. Politicians no longer cared about themselves and were focused on ensuring their people could survive. Companies realized money was useless in the threat of annihilation and offered whatever was needed.

But the big fear was that maybe this wasn't enough. The Daleks, Cyberponies, and this Black Guardian were much more advanced and powerful.

But Major-General Highmore knew humanity. Humans are a stubborn species. They would not give up. It would be over only when the last man died.

"...How are you holding up?" He turned around and saw Princess Flurry Heart looking at him with eyes no child should ever have.

"...I need a drink," He admitted.

"Wish I was old enough to have one," Flurry Heart joked, but her tone had no humor. The two stood next to each other in silence for some time. "I am sorry for your losses."

"As I am for yours," Major-General Highmore stated honestly. The word reached them of all of the attacks Equestria had suffered, and they were just as bad. So much so that Princess Luna had no choice but to order all significant cities and towns to be emptied and for all ponies to flee into the wilds. In the face of survival, material objects seemed to matter little anymore. "I've lost good men in this chaos."

"...I have lost my entire family to this insanity," Princess Flurry Heart whimpered. "My mother, father, Aunt Twilight, grandparents, Aunt Celestia, and even Uncle Spike. And now I lost my people. The Crystal Empire is gone...all of it gone..."

He looked at her and saw her doing her best to stay strong. But it was clear that there was no princess or leader. Just a little girl who lost everything she loved. Kneeling before her, Major-General Highmore slowly wrapped his arms around her and let her cry on his shoulder.

As she sobbed and wailed like a child, Major-General Highmore closed his eyes and knew at last that the Doctor was right.

It was time to do the impossible for the greater good of both their races.

It was time for an alliance with old foes.

It was time to end this war once and for all.

+}{+

There were many things that Princess Luna found terrific and fantastic about this new age she woke up to after being stuck on the moon for the past thousand years, but the greatest would always be coffee in her mind. It was the only thing keeping her going at this point. Finishing another cup, she tossed it away and looked over a long list of growing reports, needs, and messages from all their forces. With the threat of aliens attacking their homes, the division between the ponies festering for so long was now obsolete. Princess Luna clarified on a public broadcast to all Equestrians that her sister and all the other alicorns, but she and Princess Flurry Heart, were dead. She hid nothing from her people in telling them of the threat they faced and the lie that had been used to deceive them all. And she clarified that they had to work together or else they would all die.

Needless to say, nopony was willing to argue at this point.

Canterlot was not the only city attacked. The Crystal Empire was gone. There was not a soul left in the frozen wasteland. Luna didn't even bother thinking of the death toll as it was pointless. Knowing there was no chance of defending against these evil creatures, she ordered all significant cities and towns to evacuate and head for shelter in the wilds, mountains, forests, jungles, and deserts. At least there was a chance of survival if they worked together. The cities held no defenses. Not against creatures that could be fully resistant to magic.

It was ironic. A thousand years ago, Luna dreamed of being Equestria's sole ruler. Well, she got her wish. Only she lost so much in return. A princess of a broken and ruined nation that is barely holding itself together.

"Coffee?"

She turned around and saw Discord holding another large cup in both hands. The Spirit of Chaos looked like he had aged a hundred years and barely made any jokes now. He was drained not just from using so much magic to help teleport the entire population of Canterlot but also from the events in the last twenty-four hours that affected him. If what Discord told her was right, he, too, was an alien from another planet. One that was wiped out by the Daleks. She wondered if that was their fate as well?

Accepting the miracle drink without hesitation, Luna sipped and sighed. "Morale?"

"Bad."

"I figured," Luna sighed as she tossed the papers away and sat on a chair. "There is only one way this ends."

"Considering how bad the humans apparently had it with their attacks, I can't imagine they won't agree to work together," Discord snorted as he drank his coffee. "It's our own shot anyway."

"From foes who tried to eliminate each other to allies in the threat of a greater annihilation. Fate is ironic indeed," Luna muttered as she rubbed her forehead. "Is there really no way out of this?"

"No," Discord said plainly. "We're fucked one way or another. Might as well go down fighting."

"... How's Rainbow Dash's wing?"

"They had to take it off to save her," Discord sighed. "She wasn't happy about it, but they promised a metal wing as a replacement. Fluttershy, Applejack, and Rarity are doing their best to help her deal with this. As is Jolt Bolt."

"Jolt Bolt?" Luna asked curiously.

"Royal Guard who saved her life. He refuses to leave her side and Rainbow Dash is okay with it," Discord sighed. "Honestly, we all need friends in these dark times."

Luna nodded before turning outside her window to see her ponies moving with as much strength as they could, but there was a hollow silence as they did so. "I failed them. No, we all failed them. My sister and I. Twilight. Cadence. We failed them all. They looked to us to lead them, protect them. We were like gods to them. And yet we led them to ruin. How could they even look to me for leadership at this point?"

"Because you are all they have," Discord pointed out. "They got nothing else left to turn to."

"...I can't lead after this," Luna lowered her head. "Things can't be what they were before. It all has to change."

"Yes, but let's worry about that after we win," Discord pointed out as he drank some more coffee.

"You really think we can still come out of this alive?" Luna asked with a raised eyebrow.

"Of course, we have one thing that gives us an advantage."

"What's that?"

"A Doctor."

***

“There! Done all I can,” The Doctor said as he removed his surgeon mask. “Just keep him sedated for the next two hours, and he’ll be fine. Legless, but alive.”

“Thank you, Doctor. We’ll take it from here,” The Head Surgeon said as she started finishing things up. Leaving the operating room, The Doctor sighed as he wiped the sweat from his brows and looked at himself dressed in an actual doctor’s outfit. “I wonder how Grace, Martha, and Rory would react if they saw me in this?”

He shrugged and wandered around the hospital briefly to clear his head when he saw Lyra nearby looking for him. “There you are. I was wondering where you were.”

“Well, I decided the best thing to do was be my namesake and help out with the wounded,” The Doctor said with a shrug.

“I didn’t know you could perform surgery on humans,” Lyra said as she tilted her head. “How did you learn how to do it?”

“Read a few books about it in a library when I first arrived here,” The Doctor said as they walked together.

“And that’s enough?”

“For me, it is,” He said with a smile before frowning. “How are you holding up?”

“Honestly? I think I’m getting used to this,” Lyra chuckled darkly. “Is that a bad thing?”

“Try doing it for thousands of years like I do. If you ever get the moment where you just want to cry, then let it out. Trust me. It will be better in the long run,” The Doctor said as he looked at the many halls of wounded, dying, and scared humans. “It’s sad, isn’t it? So many lifeforms exist in various realities like this one, and we all keep slaughtering each other, not realizing that in moments like this, we’re the same deep down. Hurt. Scared. Confused. And wanting the pain to stop.”

“...I guess that saying about how we’re all human in the end has more than one meaning,” Lyra whispered.

“Yes, Pony or Human or insane alien traveling in a blue box. We’re all the same deep down,” The Doctor agreed before he gave a soft smile. “But it’s not just the bad things.”

He motioned Lyra to follow him. They walked for a while until they got to the children’s wing. He pushed open a door and saw many little children gather to listen to a storyteller. A particular cross-eyed storyteller.

“...And then that’s when it started raining muffins! Everyone in Ponyville looked at me, and all I could do was say, my bad!” Derpy finished her tale, which had all the kids laughing.

“That’s so funny, Ms. Hooves!”

“How did you manage to make muffins flood an entire house?!”

“I want a muffin now!”

“Tell us another story!”

“Okay! This is how I accidentally ended up in Griffinstone on a delivery to Baltimare!” Derpy said as she began the tale.

“Just because we can all cry and feel pain doesn’t mean we cannot feel joy and laughter simultaneously,” The Doctor said as he pulled out a particular amulet and saw the light blue gem glowing. He smiled. “Especially when there is always hope.”

Lyra couldn’t help but smile as well as they closed the door. “So you think we can beat the Black Guardian.”

“Yes, we have one chance. And it depends on a few things,” The Doctor answered.

“Such as?” Lyra asked, but before the Doctor could answer, a soldier approached them and saluted.

“Sir, Major-General Highmore wanted me to get you, sir. He’s agreed to an alliance with the remaining Equestrian force.”

The Doctor smiled as he turned to Lyra. “Such as that.”

+}{+

If the tension could be any thicker, you would need a buzzsaw to cut through it. Once both sides had agreed to talk about the concept of allying with each other against The Black Guardian and ending the war, the Doctor decided that the best place to have this talk was in a neutral zone. Mainly The TARDIS.

"...Impressive," Princess Luna said as she looked around the large control room. "And there are more rooms?"

"Yes, including a meeting room where Major-General Highmore is already waiting for us," The Doctor said as he motioned the Princess to join him. With her were three Royal Guards, Discord, Fluttershy, and Rarity. Applejack and Rainbow Dash were still recovering from the battle but had already blessed the alliance.

Or, as Dash said:

"Just get everything ready so I can kick this Black Guardian's flank to the void from where he came."

They traveled through the long halls, the group mesmerized by how it seemed to go on forever until they made it to a pair of double doors where The Doctor opened them. The meeting room was very spartan. A large wooden table with humans on one side and an empty side for the Equestrians save for Princess Flurry Heart. The Doctor's companions stood to the side, hopeful and nervous.

The moment they saw each other, Princess Luna and Flurry Heart hugged. For a moment, they were not the Alicorn leaders they were trying to be but the last of a broken family torn apart by madness and deceit. Nobody said anything; instead, let them have a moment to themselves.

"I am so sorry, Flurry Heart. For everything," Princess Luna whispered as she nuzzled her cheek. "I wish I had your courage that terrible day."

"I wish I could have done more," Flurry Heart whispered back as she shed tears. "But we can do more later. We...we need to fix this now."

"Indeed," Princess Luna stated as she sat across from the humans, and The Doctor sat between them. "I am Princess Luna. Raise of the Moon and Leader of Equestria."

"I am Major-General Highmore of the United Nations Armed Forces," Highmore nodded.

"Forgive me, but I was under the impression that I would be talking to one of your nation's leaders or a representative of the U.N.?" Princess Luna asked with a slightly confused tilt of her head.

"All of the U.N.'s leadership was taken by the Cyberponies," Major-General Highmore sighed, seeing as there was no point in lying. "With the world's nations trying to restore order in the attack, I have decided to take it upon myself to forge this agreement between us for our survival."

"You are not worried about punishment from your superiors?" Princess Luna asked.

"It won't matter much if we fail and all die to some evil god."

Nodding in respect, Princess Luna continued, "Then let us begin. First, I speak for Equestria, saying that our hostilities are null and void. We were deceived and manipulated into your world to cause a war that cost the lives of billions. Regardless of this deception, we still hold responsibility for it and acknowledge the wrongness in our actions. I know this is a tiny reprieve from the pain and suffering you have undergone because of us, but Equestria will spend as many generations as it takes to earn your forgiveness."

Things were quiet as Major-General Highmore stared at Princess Luna for quite some time. Nobody made a move or said a word until he finally nodded his head. "Very well. I acknowledge that the war is over. While we understand you were deceived, we will demand reparations when this is all over. I do not know what that is, but that will have to wait for another time. Regardless, I am also willing to end this war between us to deal with the bigger crisis."

"Will your fellow military officers and nations agree to this?" Princess Luna asked.

"We'll make them see. After everything that has happened, even the most spiteful of humans will have to agree that we need to work together for our own survival if nothing else," Major-General Highmore stated as the two nodded.

"Very good," The Doctor said with a smile as he clapped his hands before getting serious. "Now, to the real business."

The Doctor got up and pulled out his sonic screwdriver, which caused a panel in the wall to open up and reveal a giant T.V. screen. He turned it on, showing Earth with specific energies surrounding it. "The Black Guardian's plan is a sinister one. He seeks to bring his entire being into this universe to shape it into whatever he desires. To this, he uses the power of entropy and a complex spell ritual that requires a magnitude of death as the fuel source. We know he plans on using the Harmony Canon to do so, and while I might have sabotaged it, I'm sure he'll find a way to fix that and make it worse."

"How much worse?" Flash Sentry asked.

"Probably enough to blow up the planet in one shot."

"Ah, that is worse."

"Wait, if he destroys the planet, won't that also destroy him?" Carrot Top asked.

"Not necessary. The Black Guardian doesn't have a physical form and is mostly connected by his possession of Princess Celestia. So long as he uses that as an anchor between this dimension and ours, he'll never be stopped."

"How do we end his connection? Do we kill Princess Celestia?" Dinky asked, which made a few ponies, including Princess Luna, nervous about the concept.

"It's one way of doing it. Princess Celestia is already dead thanks to the possession; whatever of her remains is probably either gone or so crushed by the power of the Black Guardian that it holds little to no sway over her," The Doctor explained. "Regardless, I do have a plan to cut the connection. The problem is dealing with their defenses."

"Not to mention figuring out where they're going to be hiding," Princess Flurry Heart said with her wings sagging.

"Oh, I already know where they are," The Doctor said, much to their surprise.

"Where?" Major-General Highmore asked

"The only place that has a perfect shot of the Earth from where they can fire the cannon in any location," He said before using his Sonic screwdriver to reveal Earth's neighbor in space. "The moon."

"The moon?" One soldier asked. "B-B-B-But how?! You would need a huge base to-"

The Doctor used his Sonic Screwdriver to access a satellite near the moon that showed said base. It was Base Obsidian 2.0, but it was improved using a combination of Cyberpony and Dalek-based technology. The others couldn't help but gulp at the size.

"...I guess a Space Force really was a good idea," Major-General Highmore muttered. "Too bad we don't have the means to transport any forces there."

"You don't, but I do," the Doctor said with a smile. The TARDIS can get us, and she has enough room for a strong army to carry."

"That's great, Doctor, but how will we deal with the Cyberponies and Daleks?" Princess Flurry Heart asked.

"Well, we know the Cyberponies are weak against gold," Lyra said, which got stares from the ones who didn't know that. "Yeah, I know. Capitalism saves the day, huh?"

"Earth capitalism specifically," The Doctor said with a smile. "But yes, Earth gold can help us defeat the Cyberponies. The Daleks are a different story."

"How are we going to get around that? Rainbow Dash's Sonic Rainboom was the only thing that worked, but that was temporary," Princess Luna pointed out.

"Exactly," The Doctor said with a smile. "There is one weakness to the Daleks' technology. While it is highly resistant to magic, it's not fully invulnerable. A high dose of concentrated magic, unleashed in a huge wave, can act like an EMP to their systems, causing them to shut down. And we already have access to a wild source of dangerous magic that we can use to do so."

"Which is what?"

"The barrier."

This got everyone's attention.

"How will the barrier be used to defeat the Daleks?" Lyra asked.

"Didn't the Daleks attack inside the barrier anyway?" Flash Sentry pointed out. "It's not like it was fatal to them like to the humans."

"It's not fatal to the Daleks because they were inside their protective armor platforms. Outside of it, I guarantee you that the magic would prove to be fatal to them," The Doctor explained. "But it's not the inside of the barrier that is dangerous to them. It's the actual line of magic where it starts that separates the human land from the Equestrian-controlled areas. Right at that line is wild magic combined with the Elements of Harmony, Dimensional Travel, and several other powerful incarnations of magic that are still in a constant swirling expanding effort until they finally exhaust themselves, and in that case, the barrier would cease to exist. Think of it as a tsunami. Once the shifting of the plates causes a tsunami, it continues until the force exalts itself, stops, and disappears. That's exactly what the barrier is. The expanding energy of the spell used to teleport Equestria to Earth had to unleash the energy it caused and said pure energy is the barrier."

"Wait, wouldn't such a thing normally be like one big bang? Like a clogged drain being cleared and water coming out of it?" Dinky Hooves pointed out. "Or a dam opening up?"

"Oh yes, that's why Twilight's calculations for the spell to transport you all had to be perfect. One wrong calculation and both you and Earth would have blown up into smithereens," The Doctor said with a shrug.

Everyone in that room unconsciously thanked Twilight Sparkle for being so meticulous at that moment.

"Okay, you said you can use the barrier to weaken the Daleks?" Princess Luna asked, getting back on track.

"Yes," The Doctor said before getting serious. "Even with these advantages, the two races are still very dangerous, meaning we'll need to go in heavy, and we'll need to be loud. It will also take me some time to do what I need to gather the barrier energy. I will need Discord's help and the Hadron Collider. Plus, two days to do this."

"We'll use that time to prepare our forces then," Major-General Highmore nodded.

"We only get one shot at this, so we're going to have to do our best," Princess Luna replied as she got up.

The two leaders looked at each other before walking across the table. They stared into each other's eyes before Luna extended a hoof. Major-General Highmore looked at it before taking it and shaking.

The Doctor smiled.

"Well then. Let's get to work."

Author's Note

Yup, we're still going on you guys. And we're nearing the end.

As always, feel free to help out with the TV Tropes page: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse

Regeneration Part 19

"Something seems impossible. We try – it doesn't work, we try again. We learn, we improve. We fail again, but better. We make friends, we learn to trust, we help each other. We get it wrong again. We improve together, then ultimately succeed. Because this is what being alive is. And it's better than the alternative. So come on, you brilliant humans. We go again. And we win."

-The Thirteenth Doctor

"For days like this, Ruby Sunday. I don't have a people, I don't have a home... But I don't have a job, either. I don't have a boss, or taxes, or rent, or bills to pay. I don't have a purpose, or a cause, or a mission, but I have... freedom. That's why I keep moving on, to see the next thing, and the next, and the next. And sometimes... It looks even better through your eyes."

-The Fifteenth Doctor

+}{+

Major-General Highmore was a bit jealous of Princess Luna at the moment. She had reported that she had gathered all the possible forces she could bring despite the situation back in Equestria. Being a semi-worshiped leader had its perks, as anyone who believed in you would just throw themselves in front of you, ready and able to fight. Meanwhile, Major-General Highmore dealt with the consequences of living in a primarily democratic world.

"You can't be serious, Major-General?!" Colonel Spade, a veteran of the war and a friend of his, shouted as he slammed his hand on the table. Surrounding them were other members of the U.N.'sU.N.'s forces. The highest-ranking leadership that he could get in a short time, along with their troops. He sent the distress call, and they had all come. He told them what he had learned, what the real enemy was, and what they needed to do for mankind to survive. "You want us to work with the very same aliens who tried to erase the entire history, culture, and spirit of humanity on a mission to the moon?!"

"We've confirmed with our satellites that the Daleks and Cyberponies have built a military base on the moon. They are planning to use the Harmony Canon in our world. If it goes off, there is a good chance there won't be any life on this planet. Human or pony," Major-General Highmore said with a heavy sigh. "Besides, the Equestrians are victims in this as well. I'm not saying they're guilt-free with what they've done, but the real villain in all this, the Black Guardian, is the one who deceived them and made them war with us. He's the real target we need to focus on."

"Assuming this Black Guardian even exists," One Major muttered.

"Both our people got attacked by two different forms of aliens, both of which are far more advanced than us," Highmore pointed out as he nodded to the giant number of screens in their meeting room. Numerous news reports still discussed the various disasters the attacks had brought on their soil, not just in the cities that were attacked but also in those affected. The chaos and self-destruction it was causing were palpable as humanity's existence and sanity stood on the knife's edge. "Everything is falling apart, and if we don't do something, then nothing will be left to save."

The officers all looked at each other, and their torn feelings were relevant on their faces. For years, they had been fighting the Equestrians, and now they had to make peace because they were facing a threat that the two couldn't deal with on their own. It was a blow to their pride, not to mention a blow to the honor of all the lives that had been lost in the war. But Highmoore knew it would mean for naught if they didn't survive. It was no longer about anything but survival at this point.

"I'm doing this whether you join me or not, but I would like it if you were to join me," he said as he stood tall. I'm asking this not as a fellow officer or soldier but as a fellow human being. Because if we fail this, then there is no hope. We're doomed."

"...And you trust the Doctor?"

"... I've got no choice but to...and even if I didn't? Yeah, I would."

+}{+

"I want to thank you for meeting with me," Princess Luna said as she walked into her war room with three other individuals. She was sure that they would have loved to see her dead, considering what they had done to their species, but right now their mutual hatred for her was willing to be put on the backside for the sake of what needed to be talked about. "I take it you were told what was going on."

"Pretty much," Captain Celaeno said with her friends, Gabby and Pharynx, beside her. None of them had smiles. Instead, they just had glares and snarls. It was like they didn't want to be here. Not in the same room or building with those who contributed to their world's destruction.

And the elimination of their entire races save for what few remained.

"Yeah, something about a dark god that was processing your bitch of a sister and manipulated you ponies into destroying our planet, coming here to do the same thing, and now that he's exposed, he brought two deadly aliens to help wipe us all out. Now you need us to help you save your equine asses along with the humans who you tried to genocide," Pharnex said harshly before hissing. "Like you did to us."

Luna said nothing and closed the doors with her magic. "Alight. Let's get it over with. You clearly have something you wish to say to me. And I can't blame you, considering all we've done. So, for the sake of moving on? Let it out. All of it."

"... You're murderers," Celaeno growled. "Maybe not all of you, but the blood is on your kind's hooves. For all your talk of friendship and tolerance, you are the biggest hypocrites of it all. How many non-ponies had to struggle and strive to be treated with even the slightest bit of equality in your kingdom before all this? And I get it. All of our nations attacked yours multiple times at one point or another, but those were hundreds of years ago. All that did was make you think you were better than the other races back home. You showed yourselves to be selfish, intolerant, speciest, and downright self-righteous monsters who wanted everyone to be just like you. To give up our cultures, our faiths, our way of life and follow your rules because we were not "filled with the light of friendship and harmony." You thought you were better than all of us..."

"Maybe our races made mistakes and caused issues, but we still had pride. We still had good things in our lives. We had friends and loved ones and more," Gabby whimpered. "The only reason we couldn't do anything was because you controlled the sun and moon. The things we needed to survive, but instead of sharing that power you horded it. You made yourselves the top nation, and the rest of us had to bend to you, and what did we get in return? Nothing. We had to just let you boss us around, and if someone challenged you, they were seen as the villains."

"And now, thanks to you, we've all lost everything. I lost everything. My family. My friends. My entire species," Pharynx growled as a tear dropped from his eye. "You took everything from me. From us. The only reason I'm still alive and have not ended it all is that I have a new family in those who understand what I've been going through. Do you even understand what it is like for us? All of those we loved and treasured are dead because of you fucking bitches. I can understand hating us for what we did. We were enemies. But to completely destroy everything? That was too far. And even if we did deserve it, did the rest of the world deserve to freeze or burn to oblivion because of you ponies. You destroyed everything...and maybe the Black Guardian is ultimately to blame; maybe you were ignorant of it all, but we don't care. I hate you. We hate you. And we will NEVER forgive you."

There was a long moment of silence as the three stood there with rage, pain, and hatred in their eyes. And Princess Luna could do nothing but take it.

Looking down, Princess Luna sighed. "I'm not going to apologize because no apology can make up for what has happened or heal your hearts. Nor give an excuse because there is not one big enough to pardon us. I don't even think it's possible to fix this or be forgiven. You are right in all these accusations. Equestria played with fire, and in return, not only did we burn, but we burned everyone with us. Even before all this, your statements are right. We just wanted to be safe from a world of predators who could easily tear us apart...and in turn, we became what we feared."

She stood up straight and took a deep breath. "But now? The truth is that we face annihilation. All of us. I am not asking you to work for us for Equestria's sake. I am asking us to work together to survive. And for the sake of the humans who took you in. The ones who saved you and sheltered you when we tried to kill you. All of you who escaped Equestria represent the last of your races. All that they are, good and bad, lies within you. If you fall now, they are gone for good. For their legacy to live on, you must fight with us. And considering the Black Guardian was the one who manipulated us all into the situation we are now in...this is our chance to avenge them all."

She leaned forward. "You didn't survive our actions just to die now. So, are you willing to work with us or not?"

The three looked at each other before Captain Celaeno sighed.

"What's the plan?"

+}{+

When Discord learned that the Doctor needed him for whatever plan he had to deal with the Daleks, he was all for it. He wanted the chance to do whatever it took to make those bastards pay. For his parents. For his people. For all the lives that had been lost because of them. He knew this was only one small part of the most evil race the galaxy had ever seen, but it might as well have been a championship match for him.

When they arrived at sea using the TARDIS, the Doctor requested that he suck up the magical energies of the barrier and send them into a special made containing system he had connected to the TARDIS from the inside. With a snap of his fingers, one giant vacuum cleaner was summoned, and he got to work while dressed as a maid. He had made five trips with full bags before the Doctor told him this was enough. Once inside the TARDIS, The Doctor started using his console to work on the energy being kept in a giant tank somewhere else in the TARDIS.

Resting on the nearby comfy chair, Discord summoned some chocolate milk and snickerdoodles. After a bit of a bite and sip, he asked, "So, is it true?"

"What is?" The Doctor asked as he typed into the console.

"That you are the only thing that they fear?" Discord said with a smirk. "Ka Faraq Gatri. The Destroyer of Worlds."

The Doctor paused and sighed. "Yes, our little...war has gone on for a long time, since the very start of their existence. Ever since I met them, we've clashed over and over again. Every single incarnation of me has had to deal with them, and they've tried to kill me more than once. Out of all the evil beings in the universe, they are the ones I hold nothing but utter contempt for. I've seen them do countless acts of evil and do all I could to ensure the galaxy never falls to them. I've tried to eliminate them multiple times, but either my nerves failed me, or they slipped away."

He turned to Discord and sighed. "I even managed to get more lives past a normal Time Lord because of them. Sometimes, I think it's never going to end. But honestly, the idea of losing is too terrible to think about. Because I can't let them win. To let them win would see the entire galaxy cleansed in death. And I refuse to let that happen."

"...How do you do it?" Discord asked him with a shake of his head. "How do you keep fighting all this evil? This darkness. You've done it for so long...how do you keep going?"

"...When I left my home world...One of the first things I did was go to the very end...the real end..." The Doctor said as he took a deep breath and stared into the Tardis's crystal center. "I saw the end of time. The Universe. Everything. It was so quiet. So peaceful. And yet...it felt so empty. So...nothing."

He closed his eyes and took a deep breath. "And then I went to the beginning. To where it all started. One simple series of events birthed reality, life, time, space, and everything inbetween. And I thought to myself...what was the point? If it was all going to meet an end...the very same end...regardless of the choices...what was the point?"

He walked towards the doors of the TARDIS and opened them to view the sea and sky. "Then, as I traveled from world to world...past to present to future...I realized something...there was no point...so people make a point."

"Make a point?" Discord asked in confusion.

"Yes," The Doctor said as he turned around. "People make life what it is by their actions and choices. To bring peace or war. Love or hate. Creation or destruction. Discovery, invention, adventure, and experience. They create meanings and purposes for the galaxy and collide in a giant boiling pot. A near endless sea of purposes and life given to a galaxy that has none."

He smiled warmly. "It's that which gives the universe meaning. And there are always new ones every second being made. It's for that reason that I keep going. Seeing more, discovering more, and ensuring they live long enough to become a reality. The universe has a purpose. All you need to do is find one and add it to the collection."

"...I think the universe...any universe...is lucky to have a guy like you," Discord said with a warm smile.

"Well, someone has to make it interesting," The Doctor said with a smirk before heading to the console. "Now, let's get back. We still have a lot of work to do."

+}{+

Applejack knew she had to take part in preparing for everything, but there was one thing she only wanted to do. More importantly, she had one person she wanted to see. The moment she and Big Macintosh saw each other, they hugged and sobbed, not just in the relief that they were okay but also at the fact that everything they had back home was gone. From what she learned, Ponyville was abandoned. Those who saw the chaos in Canterlot had fled, and some of them managed to make it all the way to the Macintosh Mountains despite the distance. Fear can make a pony do many crazy things.

Regarding Sweet Apple Acres...well...that was also gone. Not just because there was nopony there anymore but also because Twilight decided to nationalize it when Applejack was placed in a cell. The farm, legally, was now the Crown's, and they had already started tearing it apart for mass production to feed the war effort. Only it was all pointless, with everything being what it was all. So it was all for nothing.

Applejack would have shown her no mercy if Twilight was here right now.

The two watched the ruins from atop a building in Geneva with a bottle of a drink called Jack Daniels between them. It wasn't half bad in Applejack's mind, but no Sweet Apple Acres hard cider. Taking a shot, Big Macintosh sighed. "Maybe it's for the best."

"What are you talkin' about?" Applejack asked her brother.

"Sis, we spent our backbreaking hides working and feeding an army that was trying to genocide a race that did nothing wrong to us because our Princess was being controlled by a space demon god," Big Macintosh muttered as he took another shot. "If Pa, Ma, and Granny Smith were alive, they'd be disgusted by us. Ah, don't think Ah could walk around our farm and buck a tree again there if Ah went back."

Applejack didn't say anything because, deep down, she was thinking the same thing. She took a good, long look at all the actions she had taken since they came to this world and slowly put her hat down. "What did we become?"

"Ah, don't know," Big Macintosh sighed as he handed her the bottle, and she took a big gulp. "But we can't change what happened. All we can do is change ourselves and be better."

"How can we be better after all the manure we've done to everyone? Not just to the humans, but to the other creatures back home and the ones who survived? Not to mention what we did to ourselves?" Applejack closed her eyes and shed a few tears. "Maybe we deserve to be wiped out..."

"... Ya really want to say that when yer sister and mah wife are still out there? Tryin' to come home?" Big Macintosh whispered as she wiped her eyes. "What did Pa always say when ya make a mistake?"

"Buckle up and own up to it."

"It's time we did that," Big Macintosh said as he put a hoof on her shoulder. "Maybe we'll never find true peace, but I'd rather fight trying to make up for something than do nothing and let it ruin me. We can't let this...Black Guardian son of a bitch wins. For everyone's sake... let's do the right thing for once...Yer the still the Element of Honesty. Yer are still a hero who saved us from many evils. And yer an Apple. Ya never walk away from what's right."

Applejack was quiet for a moment before she took another swing of the bottle, tossed it away, and grabbed her hat before putting it on. "Come on. We have work to do to get ready for the attack. And Ah'm not one for waitin' around."

Big Macintosh grinned before getting up himself. "Eeyup."

+}{+

The stars were bright tonight. Seeing stars from a planet was still beautiful, even if it was a different reality. The only thing more pretty was seeing Earth from the moon, which the Doctor showed her. Lyra sighed as she looked outside the window of her hotel room. Tomorrow was going to be the assault on the moon base. Major-General Highmore had gathered his forces, and Princess Luna was waiting for pick up tomorrow with her own.

The Doctor was still working on the unique weapon to deal with the Daleks, but he promised it would be done by dawn. As for the Cyberponies, golden weapons were gathered from any place possible, from spears to swords to arrows. The U.N. War Machine even made golden bullets for guns, though it wasn't enough for every soldier, so they had to carefully plan what to do. It was amazing how fast humans could make something when their survival was at stake. Thankfully, they remembered that the Cyberponies own weapons could be used against them, so it was a matter of grabbing those when possible.

Lyra closed her eyes and wondered if her life would have been any different if nothing had happened. Would she still be in Ponyville with Bon-Bon? Would she have grown closer to her and...loved her? The words of her former best friend echoed in her mind as she felt a tear drop. I'm sorry, Bonnie. I just hope you're at peace.

A knock on the door woke her up from her daydreaming, and she turned around to see Flash Sentry open her door and walk inside. "Are you okay?"

"Yeah, just...kinda getting ready, you know? Mentally," Lyra said as she got up and walked over. "Hard to believe that it ends tomorrow. All of this?"

She giggled. "You know? I didn't think this would end with fighting a dark god that represents all evil in the universe, cyborg ponies, and Nazi pepper-potted aliens. I just thought this ended with us helping humans win the war and seeing the Princesses put on trial for everything? Funny how things go, huh?"

"Sounds like one of those sci-fi novels you read," Flash chuckled.

"... We're going to win. We got The Doctor. He's the one who made all this happen..." Lyra whispered.

"It's not just him," Flash said as he walked over and smiled warmly at her. "You were the first real pony to stick up for humanity. You were the one who voiced what should have been said from the start. I think, honestly, many of us owe it to you for being brave enough to stand up for what was right."

"T-Thanks," Lyra blushed as she clopped the ground a bit.

The two stared at each other briefly before Flash coughed into his hoof. "Um, well. I better get back to bed. Big day tomorrow."

He was about to leave when Lyra dragged him back with his magic.

"...Tonight might be our last night alive..." Lyra whispered as she brought him close. "I...I don't want to spend it alone...do you?"

He blinked before sighing as he hugged her close to his chest. "No. I don't."

His lips met hers, and the rest of the night was pure passion.

Author's Note

The calm before the storm before everyone gets ready for the final battle. Only about 4 or 5 chapters left to go.

As always, please help out at the TV Tropes Pages for the Negations-Verse, including the entries for Regeneration: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse