Doctor Whooves- The Defeat

by Crimson_Moon

Rating: everyone
Tags: Adventure, Derpy Hooves, Princess Celestia, Crossover, Doctor Whooves, Twilight Sparkle, Princess Luna, My Little Pony: Friendship is Magic, Dark
Length: 9444

"I control both the sun and moon, but why do they hurt, Doctor?"-Bad Wolf. For years, The Doctor has pondered the true meaning of these words, until he came to Ponyville.

"I control both the sun and moon, but why do they hurt, Doctor?"-Bad Wolf. For years, The Doctor has pondered the true meaning of these words, until he came to Ponyville. Now, he's locked himself up in the TARDIS library to search for answers and won't come out. Meanwhile, a certain cross-eyed mare discovers a plot that threatens Equestria and all its subjects. His defeat is coming, and this time he won't be able to stop it...

Published 2014-08-26 09:00:02 UTC
Last updated 2015-01-09 06:41:35 UTC

Prologue

Prologue

“I can control the Sun and the Moon; but why do they hurt? Doctor, why do they hurt?”
-Bad Wolf

That metaphor haunted The Doctor, who didn’t understand it’s meaning until he came to Equestria. When he travelled alone, he would research on the Night and Day cycles the two princesses had control over here. The minutes he spent researching turned into hours, and the hours turned into days. Derpy Hooves eventually became concerned about his well-being, so she did the only smart thing she could think of and requested an audience with the princesses themselves. Denial after denial came through, until one day a letter arrived that read as followed:
“Dear Derpy Hooves,
I, Princess Celestia along with my sister, Princess Luna have received the many requests to be granted an audience with us. As much as we wish to help you in the matter that has arisen, we simply cannot have you come to Canterlot. A threat has been claimed on our lives and we must take every precaution to prevent our untimely deaths.”

With much sorrow and regret,

Princesses Luna and Celestia
P.S. On a more private note, we are fully aware that you are a companion of The Doctor, and it has also occurred to us the request for our audience was to seek help for whatever danger he is in. Listen, whatever is wrong; please try to seek help for The Doctor as much as you can.

After reading the letter, this gave Derpy an idea.

“Tomorrow, I’ll go to the library and see if Twilight is there. For now, I’m going to find out what he’s been researching this whole time” the mare thought to herself.

The next morning, in the TARDIS…

“Doctor, are you in here?” She said as she was approaching the library.

When she approached the doors, Derpy could hear mumbling of some sort and slightly opened the door. As soon as she did that, the mumbling stopped and she heard somepony get up from a chair and walk towards the door.

“Doctor, I’m very worried about you.” She paused for a moment, expecting a reply, but there was none so she continued.

“It’s been days since you first went in there.” Derpy opened the door all the way this time, and before her stood The Doctor, but with a dirty coat, baggy eyes, and ruffled mane.

She would have never recognized him if it weren’t for his golden eyes, gazing with hope stronger than ever.

“Not to worry, Ditzy!” The Doctor said

“My name’s Derpy…”

“Right, Ditzy! What I’ve been doing in here is researching something important and I think it corresponds with your rulers’ ability to raise and lower the sun and moon. Now if I only had the proper books…”

Derpy got a brilliant idea to get The Doctor to come with her to see Twilight Sparkle. ‘if I can convince him there are better research materials at the library in Ponyville, maybe he’ll come with me and we can talk about what it is that’s so important that he had to abandon Me, Dinky and the rest of his friends’.

“Doctor, maybe there’s a book in the Ponyville library that can help you with your research!” She said. “Great idea, Ditzy! Let’s go ask Twilight if there’s anything that can help us find what I’m looking for.”

“Oh, it’s Princess Twilight, now. You probably don’t remember because during that time we had to hide your identity from the Krillitanes.” she recalled.

So the Doctor and Derpy went to the library, which would be the start of a path neither of them could predict; One that would change their lives forever.

A few moments later at the Ponyville Library…

“Derpy, I’m glad you came by! You said there was something wrong with the Doctor, right?” Twilight asked.

“(In a hushed tone) keep your voice down! I convinced him there were research materials on the sun and moon cycles here; He doesn’t know why I really brought him. The Doctor’s in a bad state, Twilight. Just look at him! His mane is knotted up and his coat looks like it hasn’t been washed in months! Please try to help him, okay? For now, let’s keep up the act to bide us some time.” The purple mare nodded in agreement.

“I have the materials right here for you Doc-” Suddenly, The Doctor became giddy when he saw the new wings Princess Twilight adorned on her back.

“You’re an Alicorn now! How is that even possible?! Does your species have a sudden evolutionary change, and why are your wings angled? You must be considered a princess now! You should get a cane with your face on it! I think it would be the most hilarious thing I would ever see!”

Derpy's look of worry increased when she heard this.“Even his attitude is stranger than usual. I have no idea how to help him in his current state! Maybe if I just tell him about Derpy being concerned, maybe he’ll explain. After all those two ponies have been through together, I wouldn’t doubt his loyalty to Derpy.” The purple alicorn thought to herself.

Twilight thought to herself for a while, before confronting The Doctor with this. “Doctor, Derpy is concerned about you! You’ve been in your TARDIS for months on end, not leaving even once to take a break!”

He just scoffed, as if he actually thought nothing was wrong. “Don’t be ridiculous, Twilight! It’s only been a few days!” The brown stallion responded.

Furiously, Twilight yelled, “LOOK AT YOURSELF!! Your mane is as tangled and unkempt as the Everfree Forest, your coat is a completely darker shade of brown, and you’ve almost made little to no sense as soon as you walked in!”

After Twilight’s rant, The Doctor finally came to his senses a little and took a few minutes to look at himself in a nearby mirror. He was shocked at the stallion staring back through it.

“Twilight’s right. What few days I spent in the TARDIS must’ve been months out here!” the worried Derpy finally spoke.

After examining his unkempt self, The Doctor bowed his head down sorrow and began to apologize. “I-I’m sorry, I wasn’t aware that it’s been that long. When you spend a lot of time in the TARDIS, a few hours could feel like mere seconds. Honestly, I didn’t know how long I was actually in there.”

After hearing this, Twilight regretted yelling at him the way she did and apologized as well. “Now that you’ve come to your senses, could you tell us the reason behind your research? What’s so important about the sun and moon cycles?”

“Before I came to this planet, there was a friend I had. Rose Tyler was her name. One day while we were travelling, we were trans-matted onto different TV game shows on a space station, which was controlled by Daleks secretly. In order to save everyone, Rose looked into the Time Vortex itself, gaining god-like powers. This transformed her into Bad Wolf- an incarnation of the Vortex with a desire to help, no matter what the cost.” The Doctor said.

“Isn’t that a good thing, though Doctor?” Derpy asked.

“The problem is no one person can have that much power coursing through them, not even Time Lords such as myself. So, in order to save her, I had to take that power within me and give it back to the TARDIS, which acted as a conduit of that energy; That’s how it travels through time and space. The few seconds I had that power coursing within me was also enough to nearly kill me. That’s when I regenerated for the 10th time.”

Both mares listening to this story began to understand why the TARDIS was a dangerous thing if an enemy got a hold of it. “Before I took the power away from Bad Wolf, she said something that’s been itching at me ever since I came to Equestria.”

“What did she say, Doctor?” Both ponies asked simultaneously.

“ ‘I control the sun and moon, but why do they hurt?’ For 80 years, that quote was meaningless to me, just an echo from the past, but now I get it! There must be something that’s going to happen to your princesses and I think the day and night cycles might have something to do with it.”

“*gasp* I just realized, Doctor! Before I came to get you, I received a reply letter from the Princesses and it said there was a threat made on Canterlot.”

The Doctor had a smile on his face after hearing this. “Then what are we waiting for? Let’s Go!”

Author's Note

This story is specifically designed to be a fictional prequel to the origins of the painting called "Gallifrey Falls/No More" within the show "Doctor Who" and is designed to coincide with the 50th anniversary special of the show in that regard, and isn't completely done. On that note, the story is called "The Defeat" because of The Doctor's beliefs about his homeworld being destroyed during the last few days of the Time War. I'm not sure whether or not i'm going to add Doctor Hooves in the Time War to the ending chapter, but I am looking for ideas, so feel free to comment or send me some Private Messages!

History's Repeat

Chapter 1: History’s Repeat

A few minutes later, just outside Canterlot; The Doctor, Derpy and Princess Twilight begin to seek out Princesses Luna and Celestia to investigate the mysterious threat discussed in their letter to Derpy.

“Twilight, you’re close to the princesses. Is there anything they might’ve said or done to indicate what sort of danger they would be in?” The Doctor asked the purple alicorn.

“I have no idea, Doctor. The last time I saw them was after we restored the Tree of Harmony to stop the Everfree Forest from invading. Since then, they’ve been putting some distance away from any citizens of Equestria. They don’t even visit me and my friends from Ponyville anymore.” With this new information, The Doctor formulated new thoughts and ideas that might explain their unsociable behavior.

“What if they were traumatized by what they experienced in the Everfree? No, that can’t be right. I’ve seen the way they stand proud during times of distress. Maybe, just maybe this threat is from another world and they were the targets? That’s it! They’ve isolated themselves to protect their citizens!” After he was done with his thoughts, a smile of determination dawned on his face.

“Derpy, hand me that letter.”

“Why, Doctor?” She asked.

“If I am correct, this letter is a cipher to tell us the threat the princesses are facing. If they’ve been isolating themselves, it wasn’t because of standard precaution but instead are the targets of something alien and way beyond their capability to protect their citizens from the danger they are facing. Twilight, is there any secret Canterlot code the princesses used in the past to relay messages in times of distress?”

“In the diary of the princesses recovered from their old castle mentions a riddle game Luna and Celestia played. Since they were heavily surrounded by guards in separate rooms at nighttime, they would send letters that didn’t make sense if a guard read them, but if you took the 7th word of the second sentence in the letter and read them with the first 8 words of the next sentence, the riddle would be solved.”

“That’s it!” The Doctor exclaimed. “If we apply that same cipher onto Derpy’s letter, it says ‘help, a threat has been claimed on our lives.’ Now that to me sounds like they need us more than ever! Come on, it shouldn’t be that hard to find the two most powerful beings in Equestria.”

A few minutes later, in the TARDIS…

“Thanks to the cipher, now we can trace the message back to its source.” said The Doctor.

“How can it do that?” Twilight asked.

“Oh, it’s completely impossible to explain right now.” The Doctor began to look serious.

“If this threat is too dangerous even for me to handle, I need you two to go to the TARDIS. It would take an entire supernova to break through those doors and the last thing I want to happen is you two getting hurt, or worse.” The engines stopped their trademark wheezing groan, indicating to it’s passengers that they arrived at their destination.

The Doctor, Derpy, and Twilight opened the doors and saw they were in the throne room, but something felt off to the three. Sitting on the throne was Celestia, but she kept staring blankly in front of her.

“Are you alright, Princess?” The Doctor asked.

“Oh? Are you new here? I always like to see new faces!” The three ponies became confused at this response.

“Celestia, don’t you recognize me? It’s Twilight, your faithful student!” Now the Princess dawned a confused look. “You can’t possibly be my student! My student is Sunset Shimmer!”

“How many years have you been ruling so far?” The Doctor asked.

“For about 900 years. Why do you ask?” Celestia said.

“This is exactly what I thought. Someone has opened her past up like a picture book!”

“What does it mean, Doctor?” Derpy asked.

“It means the ‘danger’ they were talking about was this exact thing happening! The reason they’ve isolated themselves was to prevent any reminders that might give our unknown foe what they were looking for, which means…” Suddenly, the scene around them began to change. Celestia was still there, but seemed older and more familiar with the 3 ponies standing before her.

“Oh hello, Doctor! Is something wrong?” The ruler of Equestria asked. Other than The Doctor, the ponies in the room seemed very confused.

“Celestia, if you can hear me, give me a sign. Try to remember something, anything!” The illusion before them began to distort, revealing Celestia in real time for a brief moment.

“Doctor, help me!!! AHHH!” The seriousness of the situation now dawned on the two mares.

“Celestia! Doctor, how do I save my mentor? Please tell me!” Twilight exclaimed in a frightened and worrisome voice.

The only thing he could do was turn his head in shame. “I-I can’t, Twilight. As much as I wish I could, there is nothing I can do that wouldn’t harm you or the Princess. What we need is somepony who can synchronize Celestia’s memories in the proper order.”

The two mares now looked confused. “What I mean is we don’t have direct experience with her past” he tried to explain. “Twilight, even with that memory potion you received from Zecora you still have memories of her later years, just before the defeat of Nightmare Moon. And as for me and you Derpy, we haven’t directly intervened with her memories or her mind. We just lent a helping hand, that’s all. Our best bet is to search for her sister, Luna.”

They began to understand how much of a risk and a gamble it would be to just repair the memories all on their own. Now that they were all on the same page, the three began to look for Princess Luna in whatever condition she was in.

In a universe unknown to the three companions, a plot began to form…

“PHASE ONE COMPLETE, DALEK SUPREME.” A Dalek said.

“EXCELLENT.BEGIN PHASE TWO IMMEDIATELY.” The Dalek Supreme stated.

“CYBERMEN, WE ARE IN TEMPORARY ALLIANCE UNTIL THE ULTIMATE GOAL IS RECEIVED. IS THIS DIRECTIVE UNDERSTOOD TO YOU?”

In front of the Dalek Supreme, a hologram image formed of the Cyber Controller. “The Directive has been stated and assessed. The alliance will be formed. Cybermen are now under control of Daleks until primary directive has been neutralized. Phase Two is commencing.”

A battle map on both Cyber and Dalek ships were displayed with 3 blips in the center of what looked like a labyrinth. Suddenly with the push of a button, the labyrinth rotated and formed a new path for these 3 blips to follow. Strangely enough, at the other end of this new path was a slightly larger 4th blip.

At the same moment in the Castle…

“Shh. Do you hear that?” The Doctor said. Both Twilight and Derpy stared at him and simultaneously asked “Hear what?” Suddenly, the room began to rumble and shake, causing the roof to crack and chunks to fall. All of a sudden, the rumbling stopped.

“Interesting. Twilight, can you fly through one of the holes in the roof and tell us what you see?” The Doctor asked. She did as told and flew through one of the many holes now adorned in the ceiling.

“Good. Now tell me, what do you see?” Twilight looked around and to her astonishment saw a huge maze!

“It’s a maze!” yelled Twilight. “A giant maze! It must stretch for thousands of miles! But, how is that possible?” She flew down after describing the labyrinth to the other two.

“Just as I thought.” The Doctor said.

Derpy looked frightened and scared. “Doctor, where are we? Is this the Canterlot we know?” She asked.

“No. It’s just a clever ruse to get me to play. Well I’m not playing, you hear me?! I’m not budging!” he yelled.

“Derpy, Twilight, we’re in a labyrinth designed by my predecessors, the Time Lords. It’s an endless maze that can be manipulated and changed however they please.

“But this shouldn’t be possible! This technology should’ve been lost!”

“What do you mean, Doctor?” Twilight asked.

“What I mean is the last of these Gallifreyan Time Mazes was destroyed when my race went to war with-”. By that point, The Doctor realized who put them in this death trap.

“With who, Doctor?” both the worried ponies shouted.

He then took a big gulp and said “With the Daleks of Skaro.”

Author's Note

This chapter was one of the longest i have written yet!!!

Trapped

Chapter 2: Trapped

“Are you saying that the Daleks are responsible for capturing the two most important ponies in Equestria?!” Shouted Twilight.

“Unless the Time Lords are returning, the chances are high that they abducted Luna and Celestia and put them in this prison. I don’t know how they’ve recovered this maze, but what I do know is the threat could be extremely dangerous either way.” The Doctor thought for a moment, and looked around the room.

“Weren’t there 3 doors before I heard that noise? They couldn’t have figured out the controls that fast! Whoever we’re facing, whether it is Daleks or Time Lords, someone or rather something is guiding them and until I figure that out, we’re all just mice in a maze trying to find the cheese at the end.” He thought to himself. “It looks like that tremor we felt was the maze coming online, and the first change of routes was to this room. It looks like the only way now is forward.”

With that, they ventured down the only path presented to them. As the ponies were moving forward, they all began to feel an emotion arise and become stronger with every step. Each emotion was different for the ponies. For The Doctor, the emotion was Fear; Derpy’s was Anger, and Twilight’s was Curiosity.

The Doctor caught on to this. “I’m sure you two have noticed as well.”

“Noticed what?” Twilight replied.

“Our emotions have been tampered with. Each emotion you feel that is stronger than the others are designed to slow us down and have us quarrel with one another. Twilight, can you think of any spell to counteract with this?” The Doctor said.

“Actually, I might. During Queen Chrysalis’ invasion, Cadence used a love spell. If I could only find the original spell, I might be able to adapt it to counteract our imbalanced emotions. The problem is, only Celestia, Luna, and Cadence know the spell and one of them is being tortured, and the other two are probably still at home! Oh, Celestia! I have no idea what to do!!”

The Doctor saw something that slightly startled him. “Twilight, you might have a chance to get that spell. Look!”

He pointed to the end of the hallway, and to all three as a surprise was Princess Luna, but something seemed different.

“LUNA! Thank Celestia, you’re okay!” Twilight said as she ran to her ruler and friend. Suddenly, a dark blue wisp of magic was shot toward the sprinting Princess and was followed by a scream of pain.

“INSOLENT FOOL! Luna is no more! For I am Nightmare Moon! MUHUHUAHAHA!”

In a flash, The Doctor stood in between the injured Twilight and Nightmare Moon. With a quick flick of his Sonic Screwdriver, he shot a Paralyzing Sound-wave towards the malicious alicorn, stunning her temporarily. “Twilight, I need you to use that memory spell for your friends on Luna! It’s the only way to bring her back at this point!”

With a pain, she nodded and began to cast the spell. At the same time, The Doctor increased the frequency on his Sonic to Incapacitate Nightmare Moon’s horn and muscle functions.

“Now!” The Doctor called out and Twilight released the spell to Luna, making her remember the memories of the past few months, knocking her out after it was done.

When she regained consciousness, Luna remembered what happened. “Doctor, This was a trap to lure you here!”

“Yes I know, Luna. My suspicions arose when nopony came to escort me. Last time, your sister had me escorted by her royal guard, remember?” The Doctor said.

“Now that you recall it, I do remember. It was around the time we first met, and you were mesmerized by how I could raise the moon, just like how my older sister could raise the sun. Is that why we’re here, Doctor? Is it because of our abilities to raise and lower celestial bodies?”

“I’m afraid so, Luna. This place we’re in, it’s full of Time Lord Devices and Technology. Any number of them can be used to harness your power. With yours and your sister’s combined, it would rival the powers of a god.”

The Doctor looked around for a moment for any disguised listening devices. After he found a few, he used his Sonic Screwdriver to turn them off temporarily. “Listen, and listen carefully: whoever set this trap is incredibly intelligent. Only a small portion of the galaxy knows of my race. Even fewer know where to get their hands on a Time Maze. Your discovery, Luna, was planned. When the engines started, neither Twilight nor Derpy could hear them because it was meant to be heard only to me. You two were meant to be left clueless. After the ceiling collapsed and you revealed the maze, Twilight, upon instinct I looked around for any exits. If they wanted to kill us, why not seal off escape routes by removing the doors? No, this was planned very carefully. They wanted me to find Luna. They needed me to get cut off from the TARDIS. What this means is that whatever is at the end of this twisted path, will either try to kill us, or whoever it is will try to get us to help them.” The hidden microphone turned back on and prevented The Doctor from explaining further.

“I’m sorry, Twilight, it appears the way back to the TARDIS is blocked…” He said with an extremely exaggerated voice. The other 3 ponies became confused, so The Doctor nudged them with a worried look on his face. As soon as they noticed what he was doing, they understood and played along.

After a few minutes of walking through the Time Lord maze, the 4 ponies came across something that blocked their path…
“Doctor, what is that thing?” questioned Twilight Sparkle. What stood before them was a massive wall, which was brimming with magical energy. The Doctor was about to scan it with his Screwdriver when Luna stopped him. “Don’t do that, Doctor. You’ll only make it stronger.” She said.

“And might I ask why?” he replied.

“If you value your life, you will listen to me. This wall is known as a Gate of Tartarus, or at least a prototype.” Twilight’s jaw nearly dropped when she heard this.

“You mean to tell me that THIS is just a prototype?! It’s huge! The actual one has to be at least twice the size!”

Luna nodded. “Yes, Twilight, the actual one is much bigger, but it matters not right now. Back when Celestia and I were ruling for the first time, we devised a plan to store all of the threatening beasts that are known as myths and legends nowadays. At first, we thought putting them on either the sun or moon would be enough, but after a while, some of the more magically potent ones teleported back to the planet and again started to wreak havoc. Error after error we tried numerous ideas that expended the royal treasury multiple times, putting the nation in several periods of economic collapse and poverty. Then, a very powerful wizard came and offered a new solution. You have encountered his ancestor, Twilight. The one you call Trixie, I believe.” She explained.

Twilight was suddenly filled with envy towards Trixie. “So that’s why she calls herself ‘great and powerful’?” Twilight frustratingly said.

“Yes. He often talked about his great granddaughter with a sort of pride for her. It only made sense that she called herself those things because of her heritage. After all, her great grandfather was responsible for the design of the Gate of Tartarus. But moving on from the subject, he devised a plan for powerful wizards and mages to work together with esteemed scientists. With the geographical knowledge of volcanoes and the expertise of magical barriers, the two professions unlikely paired up and began construction of prototypes for this ‘Pit of Tartarus’.”

She continued. “After a few attempts, they successfully created one. What happened to the prototypes was unknown, until now.”

“Wait a minute, how do you just lose a door this size?!” Exclaimed The Doctor.

“We don’t know! Back then, we were a very unorganized princess and as such we just lost track of things!” Luna replied frustratingly.

“In that case, we’ll just have to find a way to tear it down.” The Doctor said.

“That’s the thing,” Luna started, “the more you try to destroy it, the stronger it gets. Even the slightest scratch will trigger its defensive mode. The earliest of prototypes, such as this one also had a major defect: its magical barrier wasn’t properly executed, so in combination with its defensive capabilities, the barrier sapped any spell caster of their energy if they so much as tried to mess with the barrier, resulting in the death of the caster. That’s why I stopped you from using your Sonic. That same barrier doesn’t know the difference between technology and magic. It probably thinks your Screwdriver is nothing more than a fancy looking wand.”

The Doctor thought for a moment. “So there were two paths we could’ve had: we could have gone back to the TARDIS and gather any resources we could before we even ventured this deep, and the one where we just started breaking down a new path for us to cross while the walls were still thin and weak. Looking at our options now, it seems there is only one left, and they won’t like what I am about to do…”

Time's Revelation

Chapter 3: Time’s Revelation

The Doctor brought out his Sonic Screwdriver and, with the push of a button, turned it on and aimed it towards the wall. The Gate of Tartarus began to groan and creak, indicating its defense mechanisms being activated.

“WHAT ARE YOU DOING, YOU FOOL!” Luna shouted out.

“I’m doing what has to be done. The way back is sealed off, and we can’t get anywhere unless this fortress of a wall is destroyed. Please no tears, I’ll be fine. In fact, this is part of the plan!” he yelled.

As soon as the Gate’s groaning ceased, its magical leech effect began and The Doctor screamed out in agony, making the three mares cry for their friend’s sacrifice. After 5 minutes of the magic tearing away his life-force, the wall began to groan again.

“(Grunts) If I could just last for a few more seconds…” Suddenly, the Gate of Tartarus collapsed, the leeching magic that affected The Doctor ceased, and he fainted from his depleted stamina. Derpy walked slowly up to the limp body that saved them, teary eyed and melancholy.

“Doctor! Doctor, can you hear me? PLEASE WAKE UP, DOCTOR! I need you…” After a few minutes of tears, Princess Luna walked up to the distressed mare.

“I’m sorry Derpy, but not even he could survive the effects of our world’s magic. The most we can do is lay the body to rest respectfully and properly. You’ve known him longer than me and Twilight. Is there any proper Funeral procedure for his race?”

All Derpy could do was nod her head in sorrow. Just then, The Doctor’s body began to glow and a golden aura was manifesting around him. In one sudden movement, he became conscious and looked at the three shocked ponies.

“Oh, hello again! Why the surprised looks? Oh right, none of you have actually seen me regenerate, have you?” They nodded. “Well then, you’re in for quite a show, because this one’s a doozy! But before I actually regenerate, do you two Princesses think you could use your horns to absorb the energy burst about to happen?” Luna and Twilight looked at each other.

“Yes, I think we can manage, Doctor.” Twilight replied. After that, the regeneration process began. In a sudden burst, The Doctor’s wounds began to heal and he was becoming reinvigorated by the second, all while the two alicorns were absorbing the excess energy.
The building shook all around them as his wounds were still being treated. Even some of the walls became torn and cracked in a few areas. After it was done, The Doctor was fully healed and didn’t have to morph into a new pony. At the same time, the two princesses’ horns started to glow a bright golden color.

“So THAT’S what your regenerative energy feels like! It’s unlike any other I’ve felt on this planet! Why if me, Twilight, and Celestia combined our power, even that wouldn’t be enough to match the strength of your regenerative energy!” Luna exclaimed.

“You’re welcome, but you might want to get that horn looked at.” The Doctor replied. After the dust settled, the room revealed was the Hall of stories, filled with murals on each side, but instead of being filled with Celestia and Luna’s stories of battle along with the bearers of the Elements of Harmony, it depicted The Doctor’s most famous adventures and battles.

“What are these, Doctor?” Derpy asked curiously. “They’re murals, but instead of them showing everything the kingdom of Equestria had accomplished, these ones show my stories- my past.” He said, looking at the first one.

“What do the titles say? It seems I can’t read them, Doctor.” Twilight said.

“*sigh* The language is Gallifreyan, only I can read them. If you’re interested in a certain mural in particular, I can translate it for you, but be warned: most of them have a deep emotional connection to me. I would advise to choose the ones that pique your curiosity the most.”

They looked around for a while, looking curiously at The Doctor’s history.

“What does this one say over here?” Luna asked. It showed a vast city, encased in a large glass dome, except the dome was scarred and in certain places it was cracked. Surrounding the city was a field of red grass. In certain spots on the grass were burned and destroyed by remnants of Dalek ships.

“It’s entitled ‘The Fall of The Citadel’.” He said.

“This was the last great city of my people, where the Time Lord Council was held. On the last day of the Time War, a device was used called ‘the Moment’- a sentient machine capable of destroying both the Daleks and the Time Lords. Needless to say it worked, leaving my race wiped out and me the sole survivor of the planet Gallifrey.”

After hearing its story, Princess Luna felt saddened by the loss The Doctor had experienced. After a few more minutes of looking, Derpy pointed out a mural that had what looked like her in it.

“Doctor, what’s this one about?” she asked. In the glass mural, The Doctor was stepping out of the TARDIS and at the same time, Derpy was greeting him.

“This one’s called ‘The Ponyville Arrival’. It’s the first time I ever came to this dimension. Do you remember? I walked out of my TARDIS and you found me. You were the one who told me I was an Earth Pony.”

Derpy giggled. “Yes, I do remember. It was the first time we met and you didn’t believe me about how there were Unicorns and how our society was Egalitarian.”

Twilight stared at one final mural: it depicted a lone stallion in the midst of a battlefield, and surrounding him were piles of corpses. This lone stallion is kneeling, weeping for his lost comrades.

“What does this one say?” She asked.

“This mural’s title is ‘The Lonesome Warrior’. It shows my grievance for each and every lost soul of Gallifrey. I regret every decision I had to make on that fateful day. With every passing century, I think about what I did to doom my people’s chance for survival, and it’s why I run. I am tired, so very tired of running. I just want a normal life without danger and destruction.” The Doctor said, with an air of sadness in his tone. There was one painting left that all 4 ponies noticed.

“Doctor, is that a 3D painting?” Derpy asked curiously. He nodded.

“How is that possible? It seems darn near impossible to me!” Princess Twilight added.

The Doctor looked at it for a moment, in depth. The painting was a depiction of a battle in the Time War, with Time Lords fighting the Daleks zooming past in their ships. In the corner in the far back, he saw a small portion of two words- No More.

“This is the most impossible painting! Like our TARDISes, the Time Lords had developed art unlike any other. The art was bigger on the inside, but sadly most of them were destroyed during the Time War. Very few survived and were lost to time and space.”

“I get that much, but what makes it impossible?” Twilight asked.

“ Ah, but what makes this painting impossible is the fact that it was made on the exact same day as the battle it depicts!”

“But how does it work?” Luna asked, curiously looking at this piece of history.

“Basically, they trap a moment in time and keep it preserved inside a bubble, well when I say bubble… It’s spacey-wacey, timey-wimey stuff you wouldn’t understand!” He responded.

Twilight, out of curiosity and intrigue, asked “What does the title say?”

“That’s odd- it has two titles instead of one. It’s either Gallifrey falls, or No More. It’s very odd that it has two. The artists must’ve had a debate about the title, so they added the most popular probably through an electoral system. I’ve always hated the long winded and boring speeches that a debate gave rise to. I’ll worry about this anomaly later. Right now, our main goal should be to get out of this labyrinth!” The Doctor said.

Far away in a Dalek ship…

“HE IS HEADING TO THE DEVICE! NOW IS THE TIME TO STRIKE, WHILE HE IS CLUELESS AND VULNERABLE!” The Dalek Supreme stated.

“No. Scans indicate he is strongest when moving towards a particular directive. We must let the plan run its course. Initiate Phase 3. His emotions are where he is weakest. Therefore, we must anger him, and make him blind to our true motives through this rage.”

Back at the Time Lord maze…
The ancient gears started turning again in the distance, transforming the layout of the maze to a new shape.

“Can you hear that?” The Doctor asked. Just like earlier, the other ponies couldn’t hear the noise, making him even more curious about the predicament they’re in.

“The gears are turning once more, and they still can’t hear it. This must be a very powerful maze if it could mask the noise of the massive machinery for normal ponies. This maze is designed to mirror certain places and contraptions from Equestrian history. I dread to find out what is ahead, but as long as I have my friends, I might be able to figure it out in time.”

Suddenly, the room they were in started to rumble and shake violently. Dividers sprouted up from the floor, isolating The Doctor from Twilight, Luna, and Derpy. A screeching noise came on, and the two alicorns started screaming in agony and passed out from the pain. “Luna! Twilight!” he screamed. The Doctor’s face was no longer showing his normal, curious self, but that of an angered god.

“Whoever is playing these tricks and hurting my friends, know this: you’ve made me very, very angry. I was planning to negotiate with you whoever you are, but now I’ll stop you and whatever you’re planning, I swear!”

Author's Note

So here's the chapter where I added the reference to the 50th Anniversary! Sorry for the delay, by the way. I was stuck with tons of school work as well as buying candy for halloween and a turkey for thanksgiving. I made sure i had time to roll out a chapter in December for you all, though! I can't tell when I'll be able to roll out a new chapter though, so just keep your lovely little ears open for the next one!

Separation

Chapter 4: Separation

Is this where I’ll die? Is there nothing I can do to save us? I can’t move-can’t breathe. Oh sister, please be okay…
In a small room, a young alicorn with at midnight blue coat and starlight mane began to wake.

“How long was I unconscious?” Luna thought.

The room closely resembled her bedroom back in Canterlot.

“Was it all a dream?” She walked towards the window and noticed there was nothing but space, not even the moon was showing.

“No, it’s real. These star patterns aren’t Equestria’s and my moon isn’t showing.”

Suddenly, the window vanished.

“YOU ARE OUR PRISONER” the Dalek Supreme stated through a projection coming out of the wall where the window was.

“But why? Why make me prisoner? You have nothing to gain from our world.” Luna asked.

“YOU ARE A FRIEND OF THE DOCTOR’S. HE WILL COME FOR YOU.” The Princess began to realize her reason of imprisonment. “What if I escape? What will you do then, ‘mighty’ Daleks? The Doctor has defeated you numerous times, and especially if his friends are in danger.”

The Dalek Supreme, now angered, screeched, “YOU KNOW NOTHING OF THE DOCTOR! HE IS THE ONCOMING STORM, THE BRINGER OF DARKNESS! EMOTION IS OF NO CONCERN FOR HIM IF THE STATUS OF THE THREAT TO HIS LIFE IS TOO LARGE!”

Suddenly a hissing sound emerged from the walls and the Cyber-Commander now took the place of the hologram image of the Dalek Supreme.

“We brought you in the maze for power over bargaining. He will destroy this Time Lord relic, but not before rescuing his friends.”

Now Luna understood the true nature of the maze.

“As long as we remain here, so will The Doctor. Which means this maze was designed for the sole purpose of separating all of us!”

In a similar room, The Doctor wakes up. “Ugh, What happened?” he thought, still recovering.

Just as in Luna’s room, a projection was displayed, but instead of the Supreme Dalek and the Cyber-Commander, the screen showed 4 different channels: one for Twilight, one for Luna, one for Celestia, and one for his most faithful companion, Derpy.

“Oh no… My friends! Stop this, whoever you are!” The screen then changed to show the culprits behind this scheme on two different channels.

“YOU ARE POWERLESS TO SAVE YOUR FRIENDS…” the Supreme Dalek said, revealing itself from the shadows.

“I should have known you were behind this, Daleks!”

In response, the Cyber-Commander revealed itself as well. “They required assistance, and we have provided the necessary components, including the parts to build your current home world’s defenses called ‘Gates of Tartarus’.”

“WE HAVE GONE THROUGH EQUESTRIAN TIME TO STUDY THE MECHANISMS” Supreme Dalek continued.

The Doctor now understood how the windows of time were opened in Princess Celestia’s personal time stream. “It took many years, but we succeeded when the directive was one and the same.”

The Doctor, getting more upset by the minute, asked “What exactly is your directive, might I ask? What could the Daleks and Cyber Ponies both want? It’s obvious that you want to rid the universe of me, but why involve this planet’s inhabitants? They have nothing of interest to you!”

They all stood in silence for a moment, until: “THAT IS WHERE YOU ARE WRONG, DOCTOR…”

Agreeing with the Dalek Supreme, the Cyber-Commander continued. “When observation began, our results were inclusive, until the painting was discovered.”

The Doctor thought for a second, recalling any time he’s seen clues to their plot.

Then it occurred to him- “Gallifrey Falls/No More… They must think they’ll get through to Gallifrey using the painting!”

“Tell me, do you plan on using Time Lord art to begin the Time War anew? Was this your plan? ANSWER ME!”

Only silence. The two adversaries let the quiet stir for a few moments. “Yes, we executed a new strategy.”

“WE ADAPTED OUR STRATEGY TO ENSURE THIS WORLD’S AND YOUR OWN DESTRUCTION.”

With a newfound sorrow in his face, The Doctor sighed. “So, that’s it. You’ve beaten me, and I don’t have anything that could stop you. Not even the Princesses can save me this time.”

Stop!

He gasped. “I thought I heard a voice! But who would have enough power left to mentally communicate?”

You have no right to give up now! I am not going to give up on you!

“Could it really be?”

In the central chamber of the maze, Celestia is being drained by the second of her magical power. With her horn glowing as bright as her sun, the Princess casts a spell to mentally link herself to The Doctor. “The sacrifices you made always inspired me to move on! Without you, I don’t think I could’ve handled keeping my kingdom intact without my sister, and you were the only one to keep me focused!”

“Is it really you then, Celestia?” he asked.

“I lend you my power, Doctor. Stop them, no matter what it takes”. The mental link finished, Celestia prepared herself for a transfer of power.
This technique was called the Alicorn Transfer, which needs an immense power and a mental link with the pony receiving it.

Luna, still in her chamber and unaware of the events taking place, suddenly sensed a rush of power fly past her. “By the Sun and the Moon! That power couldn’t have been conjured up by any Dalek contraption!”

Suddenly, the mare realized what it was. “Sister, that was your power, but if that was your power, then that means…!”

“Daleks! We demand to speak to you!” Luna burst out, hoping they were still listening. To her luck, the holograms appeared once more.

“WHAT IS THIS OUTBURST FOR?! EXPLAIN!! EXPLAIN!!”

“I surrender my power. There is no way out, and I have no other option.” She explained.

“What use is your power? Your counterpart has met the requirements to allow this vessel to function.”

Luna chuckled. “You have no idea, do you? Right now, she’s draining her power to another source. Your plan is slowly backfiring!”

Both The Cyber-Commander and the Dalek became worried, their arrogance leaving them blind to this event transpiring. With haste, they turned their attention toward Celestia’s energy-sapping prison.

“THE EQUINE LIES! THERE IS NO FORM OF ENERGY TRANSFER!”

“Explain your trickery, princess.” The Cyber-Commander demanded.

“Do you really think she’ll let you just see it? Only my power can help you detect her magic!”

Silence filled the room for a few seconds. “We comply. Surrender your power to us.”

Luna’s eyes no longer looked like they were stripped of hope. “I said I would surrender my power, but I didn’t say to you!”

Outraged, the Dalek yelled “EXPLAIN. EXPLAIN! EXPLAAAAAAIINNN!!”

“While you were looking for any variances in Celestia’s energy output, I began transferring my power!”

The Cyber-Commander, fearing the worst, asked “To where?”

She smirked. “Do you really need to ask?”

Back in The Doctor’s chamber, his power began to grow.

“I’ve had enough of playing pretend!” he said. His power steadily increasing, The Doctor grew a horn, much like unicorns have.

“You have brought with you so much death and pain! You defied the laws of time itself!”

The stallion began to sprout wings that would rival even Celestia’s. “You face before you The fury of a Time Lord!”

As a final change, The Doctor’s skin began to glow, as if he were regenerating. His spikey hair began to glow much like his coat, and turn golden, and his dark blue eyes became gold in color.

“THERE IS NO MORE POWER IN THE CENTRAL CHAMBER! THE REACTOR IS BECOMING UNSTABLE! INITIATE EMERGENCY TEMPORAL SHIFT.”
The Dalek Supreme retreated into a different region of space.

“This outcome is illogical. Initiate unit self-destruct”. The half pony robot removed its inhibitor, causing it to feel the pain of being half alive. The pain alone killed it.
I control the sun and the moon…

“I understand now…” The Doctor realized. He would have to restore the timeline. Celestia’s timeline was still tampered with.

But why do they hurt?

He focused all his energy in restoring the timeline by beginning to cast a spell he read in Twilight’s library. “They’ll have no memory of me, not even Derpy. My sweet Derpy…”

In a separate room, Twilight regains consciousness. “Ow, my head hurts…” She gasped as she felt a large energy building up. “Twilight! You are the only one that won’t be affected”

“Doctor, is that you?” She asked. “What do you mean, I’ll be the only one?”

“In order to make things right, I need to restore the timelines! Celestia’s is still tampered and the only way to fix it is to erase all traces of my travels. To them, I’ll just be a toymaker, a simple mechanic. Since you still have your alicorn power, you’ll remember me, if you want!”

For a moment, she sat in silence, feeling sorrow for what has to transpire. “There is no other way Tw-“

“DON’T YOU DARE! DON’T YOU DARE THINK YOU CAN JUST ERASE THEIR MEMORIES OF YOU! WHAT ABOUT DERPY?! SHE LOVES YOU, DOCTOR! DO YOU REALLY WANT TO GET RID OF THAT?” Twilight began bursting into tears.

“…I don’t want to abandon her, but they ensured I met my demise today. There is no possible way out of this, no way out of being defeated.”
“Then I’ll-”

“Your power isn’t enough. I’m sorry, Twilight.”

“…So this is what she meant all those years ago. *Chuckles* It’s funny how things turn out!”

“It’s what who meant, Doctor?” Twilight asked.

“An old friend of mine. Well, here goes!” The Doctor said one last time, before he cast the spell.

Screaming, The Doctor began to reset the timelines, leaving everyone affected by it with no memory of the adventures and good times they all had. All, save one alicorn princess, who had enough energy left to keep the memories alive in her mind. With a bright flash, everything was reset, and nopony knew of The Doctor, except the fact that he was nothing more than a lone stallion who lived just on the outskirts of Ponyville, who fixed clocks. They knew The Doctor as a nickname, and his real name to be Time Turner.

Author's Note

Hey guys and gals! I finished the last official chapter of this amazing journey! Quick little side note: I might add an epilogue if you want. Just let me know in the comments or by Private Messaging.

Oh, and Happy Holidays!

Epilogue

Epilogue

In a very familiar library, Princess Twilight was sound asleep, until what she thought was her nightmare woke her up.
She gasped, waking with a sweat on her brows. After the mare calmed down, Twilight looked around to find she was still in her bed in the library she came to call home. “Oh good, it was only a nightmare.” She thought. Around this time, she decided it was best to get out of bed. After making the sheets in an orderly fashion, Twilight walked to her dresser mirror and levitated the brush towards her mane in order to fix the bed head she was now wearing, when she noticed a note on the mirror signed by The Doctor.

“Spoke too soon, Twilight.”

The alicorn picked up the note and began to read it:

My dearest Twilight,

By the time you read this note, you will have thought the events that took place last night were just a nightmare. Believe me, they were very real, and you were the only one that survived the repairing of the time streams with your memory still intact. If you wish to talk about it, meet me on the outskirts of town so we can have a nice cup of tea and a chat.

Signed,

The Doctor

Suddenly, as if a storm raged inside her head, the tragic events of last night came rushing back to her.

“They… They can’t remember! Not a single one, except me. HOW COULD THIS HAVE HAPPENED?!” She sobbed. It seemed like hours on end, the only mare that could keep the memories wept for each and every pony The Doctor has saved in this world, even this universe. After regaining some composure, Twilight asked Spike to pack her saddlebags.

“Where are rushing off to?” Spike asked.

“I need to talk to a friend on the outskirts of town, Spike. I won’t be gone long, but in the meantime, you can hang out with Rarity.” Suddenly the purple dragonling became ecstatic and sped up the pace of packing Twilight’s bags.

Outside Ponyville, near a Grand Oak Tree in a clearing, Twilight waited for The Doctor…

Pacing back and forth, Princess Twilight was waiting for the appearance of the Time Lord. “Ugh, where is he? I’ve been here for a past half hour!” She said with frustration.

Suddenly, the Grand Oak Tree began to ripple, and the familiar groaning of the TARDIS’ engine began to make itself known. With a creaking of the doors of the blue box, The Doctor stepped out of the now visible time machine, looking like he did at the beginning of this adventure.

“Hello, Twilight.” He said with a half-grin, clearly suffering more than Twilight due to the things he needed to do last night. “I see you got my message. Please, come on in.”

She stepped into the TARDIS, and the doors shut behind her. Though it had the same layout, somehow the TARDIS felt different, more dark and sad looking.

“Come, have a seat in the dining room, the tea is almost ready.” He asked. “Before we begin, may I ask you something?”

“Sure.” Twilight said, becoming curious.

“Do you remember that 3D painting back on the Time Maze?” She nodded her head, recalling seeing it. “Have I ever told you why it’s impossible?”

“No, I don’t believe you have, Doctor.” The purple mare stated.

“Many years ago, possibly longer than Celestia was alive, my people went into war with the Daleks of Skaro.”

“Yes, the Time War, wasn’t it?” He nodded his head to confirm this.

“Yes. We waged war for eons, both inside and outside of time. Eventually, Daleks and Time Lords alike didn’t use strategies anymore, and just began senselessly killing one another. That is until a madman stopped them, but at a price.”

“That madman was you, wasn’t it Doctor?” With a frown, he nodded, with what little happiness he had left diminishing.

“He came across a sentient machine, capable of stopping the war once and for all. The moment, it was called.” Tears were beginning to form in The Doctor’s eyes. “ ‘No More’ he kept chanting, sending a message to both Daleks and Time Lords he had enough. With The Moment in hand, he ended the war, but at a terrible price…”

For a moment, the room stayed silent, until Twilight asked “What was the price?”

No longer able to hold the tears back, The Doctor began to cry softly. “The price, Twilight, was I had to destroy my own people! At the very last second, I began to hear faint screams as my people were burning. That day I swore I would protect anybody I could, no matter what the cost! How am I supposed to be a Doctor, how am I supposed to protect people if they can’t even remember me? I can’t do this anymore, I can’t, I-” He began sobbing uncontrollably. Trying to regain composure, he began mumbling “I’m sorry.” almost unintelligibly But to no avail.

After hearing this, Twilight began to cry softly as well, however she wanted to cheer up her friend. She wiped her tears, walked over to The Doctor, and hugged him, calming him down by whispering “it’s okay” in his ear over and over. After regaining his composure, Twilight told him something. “Now I understand why the painting was impossible, but that doesn’t matter now. Yes, your friends have no memory of the real you, but you were never truly forgotten. They know you as a toymaker, a pony who brings joy to the world, and that’s the one thing your friends will never forget. Friends may forget your face or name, but will never forget the impact you had on their lives.”

Happiness coming back to his face, The Doctor said “Thank you, Twilight. You have been a great friend to me.”

She smiled, and bowing before she left, Twilight exited the TARDIS to go fetch a purple dragon probably ogling a certain white mare with an eye for fashion.

A few days later, at the TARDIS…

KNOCK, KNOCK, KNOCK…

The Doctor, busy cleaning the TARDIS console rolled out from underneath the circuit board to see who would be knocking. “Now who could that be? It can’t be that pesky woodpecker, Fluttershy got rid of him last week!” He walked over to the double doors, and open them only to come across a red-headed mare with a rose for her cutie mark.

“Oh, hello! Is this where The Doctor lives?” Roseluck asked.

Wiping the oil from his muzzle, The Doctor said “This is him, why do you ask?”

“Well, see, I was walking along when I noticed somepony etched the words ‘BAD WOLF’ into your lovely magic tree. I’m Roseluck by the way, but you can call me rose!”

Dumbfounded both at the message, and the person delivering it, the only words he could manage were “R-Rose?” before he fainted.

Author's Note

UPDATE: I realized i made a big booboo by putting in the last bit about the new story i'm going to write in the story itself, which is against the site's policy. In order to prevent myself from being banned, i moved the story reveal in the description.

Starting in a new story altogether, The Doctor begins his travels all over again, but this time with a companion who has a familiar name, and a very familiar message from one of his old friends.

Stay tuned for the exciting story Arc dubbed “The Rose Chronicles”!

Finally got some free time to write the final chapter of this exciting story! I will be starting The Rose Chronicles, but this time I am open to suggestions! If you want to suggest something for the first chapter, please like my facebook page "Time Turner 96"(https://www.facebook.com/pages/Time-Turner-96/1375758976062686) and post your suggestions on my wall. I will be using Facebook as a hub for suggestions, because that is the only thing I will be guaranteed to see. Thank you for sticking with this story. It's my first on this site, and i hope it was a good one!