The Changeling Wars

Chapters

Distant Early Warning
The Road to War
A Good Mare Goes To War
To Befriend and Defend
Between a Diamond Dog And a Hard Place
The Chapter With No Name
Escape from Ponyville
Number 8
Trust No Pony
Crouching Pony, Hidden Changeling
Changelingville
Showdown
Epilogue

Distant Early Warning

Canterlot, Royal Courtyard
Wedding Reception of Captain Shining Armour and Princess Mi Amore Cadenza

Twilight had to hand it to Pinkie; she certainly knew how to organise a wedding reception. Sure, the pink mare had been given a rather generous budget by Princess Celestia, but Twilight could tell that every bit was well spent. She had hired Vinyl Scratch to be the event's DJ, and managed to stock the bar with signature liquor from almost every city and town in Equestria: Appleloosan Brandy, cider from Ponyville, whisky from Dodge Junction, wine from Manehattan, mead from Whitetrot, port wine from Trottingham, rum from Baltimare, vodka from Stalliongrad, and even some ale from Thunder Neigh.

She was almost too caught up in admiring Pinkie Pie's work to notice the voice from behind her.

"Twilight Sparkle, might we have a word in private?"

Twilight turned around to see Princess Luna, Celestia's sister and Cadance's mother.

"Of course, Princess. What is this about?" Twilight then asked.

"Not here. Come with me," Luna replied, leading Twilight back into the Palace. They then turned to a corridor Twilight did not recognise, and stopped at what looked like a dead end.

"Okay, is this secluded enough for you?" Twilight asked, slightly annoyed with Luna's secrecy. Instead of answering, Luna sent a pulse of energy from her horn at the wall, revealing a hidden door. Past the door was a room packed with enough high-tech equipment to put to shame Twilight's laboratory in Ponyville, or even the Flim Flam brothers' cider machine.

"This is the Canterlot War Room, one of the oldest sections of the Palace. I had it refurbished after the first sign of the Changeling threat against Canterlot," Luna explained.

"This was what you were doing instead of helping with your daughter's wedding?" Twilight inquired.

"We both know that wasn't my daughter. Until Chrysalis revealed herself, I didn't know what she was, but I knew she wasn't my Cadance." Luna retorted.

"I'm sorry I mentioned it. What did you want to tell me about anyway?" Twilight asked.

"This." The Princess directed her to the large digital map of Equestria in the centre of the room. As if it foresaw Luna's desires, the map zoomed in on Canterlot. "These readings were taken around when the Changelings were expelled from the city." Luna explained. "The changelings are represented by these black dots, which as you can see, were mostly spread out evenly across Canterlot. However, the wedding chapel is not near the centre of the city, so they were not expelled equally in all directions."

"Were you able to extrapolate where most of the changelings ended up?" Twilight asked.

"That's why I needed to speak with you," Luna replied, sending a pulse from her horn at the display table. It then played out the moment at which Shining Armour and Cadance expelled the Changelings from Canterlot. As the last one left the range of the city, the map zoomed out to show Equestria in its entirety.

"According to this, most of the Changelings ended up in the Everfree Forest," Twilight surmised.

"Yes, and the closest pony settlement to the Everfree Forest is-" Luna was about to say, before being interrupted.

"Ponyville! No!" Twilight exclaimed. She may have been born and raised in Canterlot, but Ponyville had become her home over the last two years. She couldn't bear the thought of the Changelings doing to it what they almost did to Canterlot.

"Twilight Sparkle, you are one of the smartest and most compassionate ponies I have ever met. You have more than earned the trust of the ponies of both Canterlot and Ponyville. This is why I am charging you with leading Ponyville in defending Equestria from the Changeling Horde. Do you accept this responsibility?" Luna then asked Twilight.

Twilight didn't know what to say. If she failed, she'd not only be letting Princess Luna down, she'd be letting all of Equestria down; but the Princess clearly had faith in her abilities. Even if she didn't fail, there was no way she'd have time to continue her studies and do this.

After thinking long and hard about it, Twilight finally responded with, "Yes."

"Then I hereby grant you a field commission to the rank of Commander. I know you won't let me down, Twilight Sparkle," Luna replied. "Be ready to begin preparations upon your return to Ponyville."

"There's one thing I'm wondering, Princess: Why isn't Celestia doing this instead of you?" Twilight asked.

"Equestria hasn't been at war since before my exile, so most ponies don't know that traditionally, Equestria's military concerns fall to me. As for why that is, there's a common saying in the Ibex Empire: 'The night is dark and full of terrors'," Luna explained.

"I suppose that makes sense... We should get back to the party," Twilight commented. "You should try to spend some time with your daughter before she leaves for her honeymoon."

Back at the party, Twilight tried her best to remain happy for her brother, but found it difficult with the threat of war looming over her head. She spotted Rarity and Fluttershy at the bar, and decided to join them. Seeing that Fluttershy had a Screwdriver in her hoof, and Rarity was using her horn to drink some sort of Martini, Twilight ordered a Caesar.

Rarity asked her, "Twilight, is something bothering you? You've been looking upset ever since you got back to the party."

Taking a sip of her Caesar, Twilight said, "Oh, it's got nothing to do with the wedding. It's just, I've been talking to Princess Luna, and she suspects that the Changelings are preparing for war, and they're going to attack Ponyville first."

"A war with the Changelings? Those things nearly destroyed Canterlot!" Rarity exclaimed.

"Not so loud. They're still scattered across the Everfree forest, so we do have some time to prepare," Twilight replied.

"Do you know how long we have, Twilight?" Fluttershy asked.

"No, but the Princess wants me to start work as soon as we return to Ponyville," Twilight explained. "It's the waiting that's really getting to me."

"Twilight, I know how you can get when you're under a lot of stress. I think it would help your state of mind if you did what you could for Ponyville here in Canterlot, before we leave," Rarity suggested.

"Maybe you're right. Thanks, Rarity," Twilight replied, and once she was done her Caesar, she began composing a letter to the Mayor of Ponyville.

Dear Mayor Mare,

In light of an impending Changeling attack on Ponyville, I ask that you begin preparations to have all foals, and adult ponies who cannot contribute to the defence, evacuate the town for their own safety. I will join you in preparing the town's defences soon.

Signed,

Commander Twilight Sparkle

Then, after managing to pry Spike away from the dance floor, she handed the letter to him, and said, "Spike, I need you to send this to Mayor Mare in Ponyville."

Leafing over the letter, Spike said, "Yeah, sure. Commander?"

"I'll explain later." Twilight said, prompting Spike to finally send the letter. "Let's hope that's the last surprise for tonight. I have enough work ahead of me as it is." She thought to herself.

The Road to War

Ponyville
The Next Day

The trip back to Ponyville had been particularly quiet, as Twilight had explained the situation to the rest of her friends, with each of them responding in their own way. Rainbow Dash told Twilight she'd have her full support, Pinkie Pie's mane nearly straightened, and Applejack simply wished to say goodbye to Applebloom and Granny Smith before they got sent away to Canterlot.

This awkward and unpleasant silence persisted until Rarity stepped off the Friendship Express, and stated, "By Celestia, I've never seen so many zeppelins in one place," True enough, the skies above Ponyville were full of zeppelins, and many more were parked all over the town. In a rare moment of insight, Pinkie Pie commented, "It's sad that something so beautiful can be so ominous. Balloons should be for parties, not this."

"Rainbow Dash, I'd like you to come with me to meet the Mayor in the new command centre. As leader of the Ponyville Weather Team, we could use your input in preparing the defences," Twilight said to Rainbow, while Rarity and Fluttershy were admiring the Zeppelins.

As the two mares entered the new basement-turned-war-room in the Town Hall, they could easily see its unfinished state. One of the first things Twilight noticed was the digital display table in the middle of the room, much like the one in Canterlot. Unlike the Canterlot War Room, however, most of the other equipment was still in the process of being installed. Twilight then turned to the Mayor, to see her standing at the display table with the most nonsensical and daydreaming pony in town: Derpy Hooves

Mayor Mare declared, "Welcome back to Ponyville, Command-"

The mayor was interrupted by Derpy shouting, "Hi, Twilight!"

In a way, Twilight was relieved; she still wasn't entirely comfortable with ponies referring to her as "Commander". "Um, hi, Derpy. What are you doing here?" Twilight asked. In some ways, the wall-eyed pegasus reminded her of Pinkie at her most erratic.

"I'm your second in command," Derpy explained, fiddling with a few controls on the display table.

"You are?" Twilight asked, having trouble believing what the mailmare was saying.

"Yes! I was hoofpicked by Princess Luna herself," Derpy answered.

"Well, I suppose Luna knows what she's doing," Twilight commented.

"Here, take a look at this," Derpy then said, pointing at the display table. The map of Ponyville now featured several numbers scattered across it, in red, blue, and green.

"Okay, what am I looking at here?" Twilight asked.

"Red indicates locations for gun turrets, blue represents buildings that need to be shielded, and green represents locations for screeners, and the numbers indicate importance." Derpy explained, starting to show some method to her madness.

"Screeners?" Twilight inquired. It was the first time she had heard the term.

"I can answer that. A screener is a type of doorway designed to identify Changelings. If a disguised Changeling passes through a powered screener, its disguise falls apart, and its true form is revealed," The Mayor piped in, playing a video on the one wall-mounted display that had been installed to demonstrate. "The design was tested on captured Changelings in Canterlot, so we know it works. However, it also disrupts all types of magic that pass through it. Anything that passes through it would briefly be rendered magically inert. This way, a Changeling can't simply re-assume its disguise right after going through, or lash out with magic. Of course, it has same effect on unicorn horns, and it causes pegasus wings to lock up."

"I see." Twilight commented, taking a further look at Derpy's setup, seeing that it was far more thought out than she had initially expected.

"I'm impressed, but I doubt Fluttershy is going to happy about her cottage being the #1 spot to place turrets." Twilight commented.

"I know, but it's the closest property in Ponyville to the Everfree Forest." Derpy retorted.

"Ok, but what about the woods surrounding Sweet Apple Acres? If the Changelings cut through that, they'll be right on our doorstep." Twilight asked.

"I've been thinking about that. Turrets are going to be useless in there; there's too much cover, and mines would cause considerable damage to the town's food supply." Derpy commented.

"Not necessarily. I could rig storm clouds to go off on proximity rather than contact. I call it a Lightning Mine." Rainbow Dash suggested.

"Good idea. I want you and the Weather Team setting up your Lightning Mines all over those woods. Just be careful." Twilight instructed Rainbow Dash.

"You got it, Twilight," Rainbow replied, flying out of the room.

"Now, what's our best estimate on how long we have before the Changelings attack?" Twilight asked Derpy and the Mayor, once Rainbow had left.

"According to our long range sensors, around a week," The Mayor answered.

"That doesn't give us much time, so let's make the most of it," Twilight commented, turning to Derpy, "Derpy, you know I gave the order to have the town evacuated; has Dinky been sent away already?"

"My husband's taking care of it," Derpy explained.

The mailmare's answer seemed vague, so Twilight then asked, "What do you mean?"

"The Doc- Time Turner is personally making sure Dinky is safe," Derpy elaborated.

Twilight couldn't help but notice how Derpy corrected herself when stating her husband's name, and that she had said "my husband" as opposed to "her father", but decided not to press the issue.

"Okay. I suppose the next order of business is to figure out how we're going to construct our turrets, screeners, and shield generators," Twilight stated.

"Don't forget the gunships!" Derpy added.

"Is there anything else the Princess has neglected to tell me?" Twilight asked rhetorically.

Sweet Apple Acres

Sweet Apple Acres was a sad sight. A zeppelin was parked just outside the barn, and Twilight, Derpy, and Spike managed to arrive just as Applejack and Big Macintosh were saying goodbye to their grandmother and little sister.

"It'll be alright, sugarcube. You'll be back here in no time," Applejack tried to reassure Apple Bloom, but she had trouble believing it herself.

Twilight decided to give them a moment before she approached. "Scenes like this are playing out all over Ponyville. On my order." She thought.

Before Twilight could say anything, Applejack turned and beat her to it. "Oh, hey Twilight, Miss Hooves. What can I do for you?" She asked.

Twilight was about to answer, but she was cut off by three familiar voices shouting "Yay! Cutie Mark Crusader Refugees!" from the zeppelin.

"We need your help in preparing Ponyville's defences!" Derpy blurted out.

"We'll do what we can, but I'm not sure how much we can help y'all. We don't have much in the way of horsepower or resources, and the best Apple to help you just got sent away to Canterlot," Applejack responded.

"Listen, I'm sorry about that," Twilight replied.

"Don't be. You were right to send them away. Ponyville just ain't safe anymore, Sweet Apple Acres least of all," Applejack reassured her friend. "Honestly, though, I don't see anyway to get the defenses ready in time."

"Um, actually-" Big Mac suggested.

"No way! They caused enough trouble the last time they were here! I'd sooner hoof Sweet Apple Acres over to Queen Chrysalis herself than work with them!" Applejack shouted.

"Who are you talking about?" Derpy asked, slightly confused by Applejack's reaction.

"Who do you think?" Applejack responded.

"Applejack, they're the only ponies who can work quickly enough for us to be ready in time for the Changeling attack." Twilight reasoned.

"Oh? And what if those two do something stupid like cut the quality control again?" Applejack retorded.

"They won't. If we lose, they lose." Twilight pointed out.

"Fine." Applejack conceded.

Twilight then turned to Spike, "Send a letter to the Flim Flam brothers. Tell them what we need, and to meet us in the Ponyville War Room." She instructed.

"Time Turner could help. He's really good with advanced technology. And there's our friend Mjölna, too. She's a great mechanic." Derpy suggested.

"Good. Have them meet us in the War Room as well." Twilight replied.

Ponyville War Room

Twilight had her team, plus Flim and Flam, gathered in the War Room to discuss the best means to construct Ponyville's defences. The difficulty in working with two stallions who had tried to run the Apple family out of town, only to get run out of town themselves, was evident in everypony's faces.

After examining both the blueprints and Derpy's map, Flim looked up from the display table, and said, "Well, Commander Sparkle, it's a tall order, but we should be able to modify the design of the Super Speedy Cider Squeezy 6000 to create suitable assembly lines for these machines."

"So you'll help us?" Twilight asked.

"For the right price," Flam answered. "5000 bits per gunship, 4000 per turret, 2500 per shield generator, 1000 per screener, pull 100000 bits initial setup costs for each assembly line."

"Ah should've known. Typical businesspony attitude," Applejack muttered.

"Costs like that could bankrupt Canterlot!" The Mayor commented.

"You expect to charge that after your cider?" Time Turner angrily asked.

Before the argument could descent into a full-out brawl, Twilight spoke up. "Listen to me, you two. When the Changelings begin their invasion, they're going to hit Ponyville first, and as long as we can hold them back here, we can keep them from attacking the rest of Equestria. If Ponyville falls, Equestria falls with it, and profiteering like this helps nopony but the Changelings."

"You make a fair point, Commander, but don't expect us to work for free," Flim conceded.

"I wasn't going to," Twilight replied. "I want Mjölna and Time Turner here to work with you. She's one of the best mechanics here in Ponyville, and he's an expert on the design side of things."

Time Turner and the sand-coated Earth pony then joined the two unicorn brothers as they left the war room. Just before Mjölna walked out the door, Twilight leaned over, and whispered, "Keep and eye on them, and make sure they don't try anything."

"I still think you're makin' a mistake in hiring them, Twilight, but it's your call. For what it's worth, I trust you." Applejack commented.

"Thanks, Applejack," Twilight nodded, forcing herself to smile.

Once the others had left the War Room, Derpy suggested, "Now might be a good time to send the Princess a report on our progress."

"Good idea," Twilight responded, turning to Spike, "Take a letter, please."

Dear Princess Luna,

I am happy to report that preparations for the Changeling attack are ahead of schedule, and we should be ready for them well before they're expected to arrive. I've secured a deal with the Flim Flam brothers to produce weapons and other defensive measures for us, and evacuations should be complete by tomorrow afternoon.

I must admit that I had my doubts about your decision to appoint Derpy Hooves as my second in command, but these doubts quickly proved to be unfounded. Her reputation here in Ponyville is less than stellar, and most ponies assume she is less than intelligent due to her eyes. While she can be a bit clumsy and absent-minded, it couldn't be farther than the truth. She clearly has a strong understanding of the layout of the town, and of the best ways to set up our defences. I doubt I could have done nearly as much without her help. There is no better pony I could think of to be my second in command.

Your faithful soldier,

Commander Twilight Sparkle

After Spike the sent the letter out, Twilight couldn't help but think to herself, "This is just going to get worse."

A Good Mare Goes To War

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Ponyville War Room
Five days later

Sipping on her cup of coffee, Twilight pondered on the work she had been leading over the past week. In many ways, it felt like an affront to everything Equestria stood for. This wasn't the town she had fallen in love with. This place was armed to the teeth, there were no families, only ponies capable of fighting, and nearly every important building had magical shielding over it. Each of her close friends had their own part to play: Rainbow Dash was leading a team of Pegasi, engaging the Changelings hoof to hoof to in the air, Fluttershy was operating the gunnery position near her cottage, Rarity was maintaining the shield over Town Hall, Applejack was piloting the lead gunship, and Pinkie Pie was serving as one of her gunners, along with Caramel and Big Macintosh. In accordance with her position, Twilight had donned a black military jumpsuit, while Derpy now wore an eyepatch, to keep ponies from being distracted by the problem with her eyes.

She was almost spat out her coffee when Derpy shouted, "Twilight! We've got movement!"

Snapping out of it as quickly as she could, Twilight then asked, "Where?"

Checking the display table, Derpy answered, "They're trying to go through the minefield!"

Then, opening a comm channel with Fluttershy, Twilight called out, "The Changelings have entered the minefield; be ready to open fire at any moment!"

Fluttershy's Cottage

"I wish I had been with the ponies who left for Canterlot," Fluttershy thought as she heard the order from Twilight. While she had volunteered for the gunner position at her cottage, it didn't make the experience any better, or the waiting any less nerve wracking. She shuddered as she heard thunder coming from the woods south of her, and the fluttering of countless, pony-sized insectoid wings to the west of her. As the sounds got closer, the butterflies in her stomach built up, until she got a visual on the Changeling Horde, at which point, she took a deep breath, and squeezed down on the triggers.

The turrets let loose countless bolts of magical energy into the oncoming horde. While she managed to make short work of the Changelings she did hit, there were simply too many, and most of them flew past, heedless of Fluttershy's gunfire.

War Room

"Twilight! There's too many of them!" Fluttershy shouted over the comm.

"Are they going after you?" Twilight asked.

"No, they're just flying past," Fluttershy explained.

"Then keep firing; it'll lighten the load for everypony else," Twilight instructed, turning to the Mayor, "Give the order."

"Changelings have breached our first line of defence. Scramble all gunships! I repeat, scramble all gunships!" the Mayor called out over her microphone.

Sweet Apple Acres

"Read you loud and clear, Miss Mayor!" Applejack responded. While she knew the Mayor wouldn't hear her, it seemed appropriate to acknowledge the order. As she lifted her gunship off the ground, the other gunships began to follow suit. The eight gunships leaving the main barn at Sweet Apple Acres then lifted up above the trees, clearing the minefield and moving to intercept the Changelings at the clocktower.

Even with the gunships coming in from other parts of the town, they would be vastly outnumbered by the Changelings, but what the ponies' gunships lacked in numbers and manoeuvrability, they easily made up for in firepower and durability. Each gunship was fitted with two frontal cannons, plus an additional gunnery position on each side, not counting the horns of any unicorns on board, while the Changelings only had their horns for ranged combat. Even then, it would take several shots to down a gunship, while one was enough to rip a Changeling apart.

Unfortunately, the gunships were not able to reach the clocktower in time, and the Changelings soon overran it, using it as a starting point to spread across the rest of Ponyville.

Applejack then heard Twilight's voice over the comm, saying "All gunners, fire at will!", followed by an expected "Eeyup" from her brother, an "Okie dokie lokie" from Pinkie Pie, and a "Yes ma'am" from Caramel. The four of them then opened fire on the Changelings, ripping some apart, while only sending others to the ground. As one hit by Pinkie Pie fell, it cast a shield spell on itself, allowing it to hit the clock tower with enough force to topple it.

War Room

"This is descending into chaos too quickly," Derpy commented, watching the feed of the clock tower's destruction.

"Gunships, concentrate your fire on the clock tower; that's where the Changelings are the most heavily concentrated." Twilight instructed. Switching channels, she then said, "Rainbow Dash, I need your team ready to to take out any that get past the clock tower."

"You got it, Twilight!" She heard in response over the comm.

Sugarcube Corner

The Changeling Horde managed to reach Sugarcube Corner before being intercepted by Rainbow Dash's Pegasus Attack Force. "Pegasi, attack!" Rainbow Dash called out to her team. The Pegasus Attack Force then engaged the Changelings, supported by the nearby ground turrets.

Amid the carnage, Rainbow Dash spotted one of the four nearby gunners jump out of her post and make a run for Town Hall.

"Vinyl! What are you doing?" One of the other gunners shouted at her.

"Following orders, Octavia!" Vinyl shouted back at her.

"What is Twilight planning?" Rainbow Dash thought to herself.

A Changeling then took the opportunity to attack Rainbow Dash, but was quickly shot down by another one of the gunners.

"Thanks, Lyra!" Rainbow Dash called out.

War Room

"Vinyl's on her way, just as you instructed," the Mayor informed Twilight.

"Good. There's too many of them for us to just keep picking them off." Twilight replied, opening up a channel with Rarity in the generator room. "Rarity, be ready to lower the shield on my signal." She instructed. "Let's hope this works." She then thought to herself.

Sugarcube Corner

Rainbow Dash watched in horror as Thunderlane took several shots of Changeling Magic to his wings, and fell to the ground. He was in serious pain, but he was still alive. Then, four Changelings circled in on him, taking the form of his little brother Rumble. They started to feed, and ... nothing. They just reverted to their true form and flew off again. Coming to his aid, Rainbow Dash made a mental note of this, suspecting Twilight would want to know. She hoisted the black pegasus up by his front legs, and started carrying him to the hospital, with the three remaining gunners, Lyra, Bon Bon, and Octavia, covering them.

Ponyville General Hospital

Just as Rainbow Dash expected, the hospital was already flooded with wounded, but she didn't expect it to be as bad as it was. "After all, they do want us alive. Why haven't they made an attempt here yet?" She thought to herself, then she remembered how the Changelings had simply ignored Thunderlane after he fell.

Two medic ponies were ready with a stretcher for Thunderlane at the entrance. As Rainbow Dash set him down, one of the medics, a green-coated unicorn stallion, asked, "Shot down by the Changelings?"

"Yes. Apart from the scorched feathers, I suspect he's got cracked ribs, broken hind legs, and head trauma," Rainbow Dash explained.

"We'll do everything we can." The medic replied. They then carried him into the hospital, and Rainbow Dash flew off, returning to the fight.

Clocktower Ruins

Applejack's gunship circled the wreckage of the clocktower, laying down suppressing fire in all directions. Pinkie Pie noticed that the number of Changelings flooding in was starting to die down, and the persistent sound of gunfire from the west told her that Fluttershy was still alright. Taking a quick look at the destroyed tower, she thought to herself, There's no way a Changeling could destroy that just by colliding with it. Knock a hole in it, maybe, but not topple it. She then saw a gunship, operated by the trio known as the Flower Ponies, take a serious hit to its starboard engine, and begin spiralling to the ground. Fortunately, all three of them managed to eject in time. However, their starboard gunner, an Earth pony named Noteworthy, wasn't so lucky.

War Room

"The Bass Cannon is in position, and ready to fire," Vinyl informed Twilight over the comm.

"Good. Rarity, drop the shield," Twilight then instructed.

"Let's hope this works," Derpy commented.

The light blue bubble protecting Town Hall dissipated, and nearly all of the Changelings in the town focused their attention on it.

"They're approaching Town Hall, just as you predicted," The Mayor pointed out.

"Wait for it," Was all Twilight said in response. The closer the Changelings got to Town Hall, the closer they got to each other, and the more of them would be caught in the Bass Cannon's blast radius.

"They're getting closer!" Derpy called out, starting to panic.

"Wait for it." Twilight said again.

"TWILIGHT!" Derpy finally shouted at her.

"Fire!" Twilight finally called out. Then, they all heard a massive repetitive 'wub' sound from above, quickly building in intensity until it formed a massive beam of sonic energy, tearing away any Changelings in its path. Any Changelings that escaped the blast flew back to the Everfree Forest, while any that simply survived slowly retreated on hoof. Twilight breathed a sigh of relief; they had managed to drive the Changelings back ... for now.

Some Time Later

"I want more fortifications around the hospital. The Changelings haven't made any moves on it yet, but I don't want us taking any chances." Twilight instructed the Flim Flam brothers.

"You're one to talk about taking chances, Twilight." Rainbow Dash commented. "They're not interested in the hospital, anyway."

"What do you mean?" Derpy asked.

"After Thunderlane was shot down, the Changelings tried to feed on him, but it seemed as though they couldn't. My guess is that for whatever reason, physical pain protects ponies from being fed upon."

"Interesting." Twilight commented, though unsure of how to use that to Ponyville's advantage. At that moment, Pinkie Pie barged into the War Room, followed by a much calmer Applejack.

"Twilight! We have a problem!" Pinkie shouted.

"What is it, Pinkie?" Twilight asked.

"We can't account for all of the Changelings in the attack." Pinkie explained. "Look." Pinkie then plugged a set of figures into a nearby console, and then the numbers came up of one of the wall mounted display screens.

"Here's the problem, Twilight: We managed to get a count of all of the downed Changelings, the dead Changelings, the captured Changelings, and Changelings that retreated back into the Everfree Forest." Applejack clarified.

"And?" Twilight asked.

"It doesn't add up. There's about twenty Changelings unaccounted for." Applejack explained.

Twilight shuddered at the thought. One Changeling infiltrating the town was bad enough, but twenty? Even with the screeners in place all over the town, they could still do plenty of damage.

To Befriend and Defend

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War Room
Two Months Later

"How big is it?" Twilight asked Derpy, who was examining the long range scanners.

"It's big. Maybe even bigger than their first attempt," Derpy responded. Over the past two months, the Changelings had continued their barrage of skirmishes against Ponyville's defences, but in much smaller numbers than their first attack, and the ponies were always able to drive them back with minimal casualties on their side. However, with each repelled attack, the number of unaccounted for Changelings grew. Ponyville's defence team had every reason to be concerned; the number of Changelings they couldn't account for was now almost at 200.

"Applejack, prepare to launch gunships!" Twilight instructed over the comm.

Sweet Apple Acres

Applejack's gunship squadron lifted off the ground, but just as they were about to leave Sweet Apple Acres' airspace, the two gunships flanking Applejack were shot down by the turrets at the barn door. Pinkie Pie and Caramel quickly returned fire, making short work of the hijacked turrets.

"Mayday, mayday! Changelings have infiltrated the defences. I repeat, Changelings have infiltrated the defences." Applejack sent out on an open channel.

War Room

"This is bad, very bad." Twilight commented, checking the display table and finding several similar occurrences throughout the town.

"The Pegasus Attack Force will need to be especially careful," Derpy pointed out.

"They'd have gotten the same warning as everypony else; what we need now is a visual on Fluttershy's cottage." Twilight instructed. Flim then changed the main screen's input accordingly.

Fluttershy's Cottage

Fluttershy trembled in the seat of her turret. Sure, she had gotten used to firing upon the Changelings attempting to invade Ponyville, but this time, it was different. This time, they were headed straight for her. While she was able to stop a few of them, her gunfire did little to stop them from divebombing the turret itself. Seeing the Changeling headed straight for her, she jumped out of her seat and flew to safety as it tore through the turret. She lacked even a moment's respite, as one of Ponyville's own gunships flew past. Rather than firing upon the Changelings in the area, it took several shots at Fluttershy's cottage, reducing it to smoulders. However, she recognized the pilot and the gunners, and she knew all of them were supposed to be operating ground turrets, not a gunship. Flying to a secluded spot, Fluttershy sent out a message back to the the War Room.

War Room

The team in the War Room, including the Mayor and the Flim Flam brothers, watched in horror as Fluttershy's home was destroyed.

"Fluttershy, come in!" the mayor shouted over the comm.

"I'm alright. I made it out just in time," Fluttershy replied, static slightly garbling her message.

"Good. If you can, find Rainbow Dash and join her attack force," Twilight instructed.

"It looks like they have their own problems, Twilight" Derpy commented, pointing to the Carousel District on the display table.

Carousel District

Rainbow Dash's team made their way through the streets, believing themselves to be ready for the Changelings. Even with the news of Changelings infiltrating the defences, Rainbow Dash still wasn't expecting Flitter, still in attack formation, to make a move on her. She quickly realized what was going on, and slammed one of her front hooves into the fake Flitter's face, followed by a quick buck at the base of her wings, sending her down to the ground. Unfortunately, the Changeling's horn lit up, evidently in preparation for a divebomb, and ended up blowing a massive hole in Carousel Boutique.

Rainbow Dash now wondered who else in her team could be a Changeling in disguise, and realised the problem would be worse for her and the pegasi in her team than it would be for anypony else. She looked back at the rest of her team, and took note of the expressions on their faces. "Is it paranoia I see in their eyes, or the fear of being exposed prematurely?" she thought to herself.

To make matters worse, it looked as though Blossomforth and Cloud Chaser were about to start fighting, as if each suspected the other of being a Changeling. "Odds are neither of them are." Rainbow Dash thought. Just before it came to blows, she then gestured to Snowflake, and the hulk of a pegasus grabbed both of them, and gave them each a stern look in the eye, silently telling them to break it up.

"Keep an eye out. The Changelings are enough of a problem without us turning on each other." Rainbow Dash then said to Snowflake.

"Yeah." He responded, much quieter than usual.

"I can trust him. It would be difficult for the Changelings to mimic his form." Rainbow Dash thought.

Sugarcube Corner

What was left of Applejack's gunship squadron managed to intercept the Changelings at Sugarcube Corner, but they were too late to save Sugarcube Corner itself. The establishment was burning from the bottom up, and there were already several holes blown in the sides of it.

"No. No!" Pinkie Pie shouted. "At least the Cakes can't see this." She thought, but it was her home too, and losing it was enough to deflate her mane. In an almost blind rage, she opened fire, mercilessly gunning down any Changelings in view. The hail of magical gunfire persisted until Pinkie's guns overheated and knocked her to the back of her seat.

More Changelings flooded in from west of the town, but Pinkie's outburst gave the Pegasus Attack Force the opportunity it needed to break through to the front lines. Despite being reduced in number, and on edge from suspecting each other to be Changelings, they still fought with great ferocity against the actual Changelings.

War Room

"It appears we're actually driving them back." The Mayor commented. "We may still win this one."

"Good. Vinyl, get the Bass Cannon ready." Twilight instructed.

"No can do, Twilight. Damn thing's burned out. I'm guessing sabotage." Vinyl sent back.

"That wouldn't surprise me." Twilight thought.

"Twilight! Look!" Derpy called out, pointing to the camera feed from near Fluttershy's ruined cottage. Out of the dense foliage of the Everfree Forest, Twilight could see the unmistakable outline of the Queen of the Changelings herself.

"She's here," was all Twilight could say in response.

As if on cue, the shields over Town Hall dropped without warning. "Rarity! Get the shields back up! Now!" Twilight called out over the comm. No response.

"Derpy, get me the camera feed for the generator room." Twilight instructed, but as Derpy brought up the feed, all it showed was static.

"I'm going to try the last thing it recorded. That might tell us something." Derpy suggested. This time, what came up was a video of Rarity, maintaining the shield, like she was supposed to, until she took a hoof to the back of the head, and fell unconscious. As Rarity fell to the floor, her assailant revealed herself to be another Rarity, who then used her horn to destroy both the shield generator and the security camera.

"But that means the screeners are-" Twilight said as she realized her mistake.

"Fake." Flim finished her sentence. In a unprecedented moment of anger, the Mayor charged at the Flim Flam brothers, only for Flam to fire several shots at her from his horn, killing her in a matter of seconds.

"Honestly, Commander, we should be thanking you for making it so easy for Queen Chrysalis to counter your offer." Flim continued.

Panicking, Twilight made a mad dash for the microphone hooked into the PA system, but it was cut short after Flam fired another shot of magical energy from his horn. This time, it hit Twilight in her right eye, and she screamed in pain as she fell to the floor.

"Trying to warn Ponyville? I don't think so." Flam taunted, but Twilight was too focused on the searing pain to notice. Though she had lost the use of that eye before, the pain was much worse this time. Between that, and the sight of Mayor Mare's body, she was almost certain the damage was permanent.

Even over the pain, she did hear the sound of wood shattering above them. "That should be the Queen now." Flim commented nonchalantly. Twilight thought back to the last time she saw Queen Chrysalis; not even Princess Celestia was a match for her. What could a one-eyed unicorn in shock and a wall-eyed pegasus do against that kind of power? Twilight trembled as Chrysalis entered the War Room.

"Twilight Sparkle, I've been looking forward to meeting you again," the Changeling Queen said, maintaining her melodramatic tone. "You have so much love for me to feed on. But who to start with?" Chrysalis asked. "Your friends?" She said first, shifting between the forms of Pinkie Pie, Rainbow Dash, Rarity, Applejack, and Fluttershy. "Your family?" She said next, shifting between Twilight's parents, and Shining Armour. "Royalty?" She then shifted between Princesses Celestia, Luna and Cadance. "Or maybe that schoolteacher you're so fond of." Chrysalis finished, settling on the form of Cheerilee.

"Not her." Twilight thought, terrified of what would happen to her if Chrysalis managed to feed. Chrysalis approached with a malevolent green glow in her eyes, but the glow fizzled out as she got close enough to feed.

"Nothing? No, it's there, I just can't get at it." Chrysalis said in Cheerilee's voice, before reverting to her true form. Angrily, she turned to the Flim Flam brothers and shouted, "You had to shoot out her eye, didn't you? She's useless to me like this!" She then turned back to Twilight. "Perhaps a taste of your brother's medicine is in order instead." Chrysalis said, charging up her horn.

Just as the spell fired, Derpy jumped in the way of it, causing it to launch both her and Twilight out of the War Room and into the unknown.

"Idiot," Chrysalis muttered as she stepped up to the PA system's microphone.

Activating it, she announced, "I really must commend you all for your valiant efforts in defending your quaint little town. I never thought ponies were capable of such violence. A shame it was all for nothing. Drop your shields, lay down your weapons, and welcome to Changelingville."

To Be Continued...

Between a Diamond Dog And a Hard Place

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"Twilight? Twilight?" Twilight heard faintly as she regained consciousness. She slowly opened her good eye to see Derpy standing over her, and the two of them appeared to be in some sort of desert.

"Thank Celestia you're alright. You've been out cold for three days; I can't believe how lucky we've been," Derpy exclaimed.

"Lucky? Lucky?! We're stranded in the middle of a desert and I'm missing an eye! How exactly are we lucky?" Twilight demanded.

"First of all, you're lucky Flam shot you with his horn and not a gun, because this way you don't have to worry about losing any blood. Second, we're lucky I was able slow us down enough to land safely," Derpy explained, then adding, "About your eye, take my eye patch. You need it more than I do." Derpy took off her eye patch and handed it to Twilight, who then magically put it on over what was left of her right eye. Thinking that she probably looked similar to the "Future Twilight" whom she met once, the unicorn chuckled for a second. However, that chuckle died away quickly, when she remembered that her eye patch was going to stay on her face forever this time.

"What is it?" Derpy inquired.

"I was just remembering how about four months ago, I was visited by myself from the future, and she, or I, looked a lot like I do now. I even asked her if there was some sort of epic pony war in the distant future," Twilight elaborated.

"She tried to warn you about this?" Derpy asked.

"No. As it turns out, she was from the following Tuesday, and she only looked the way she did because of a bunch of random injuries over the week," Twilight finished. "Now, where are we?"

"Well, the last town I saw before we landed was Appleloosa, but it looks like a four day walk from here," Derpy answered. Twilight wasn't sure how to feel about that. Chrysalis had evidently managed to launch them from one end of Equestria to the other. On the other hand, there was no way the Changelings could have made it this far yet.

"Let's get moving then," Twilight finally said, before hearing her stomach grumbling. "You wouldn't happen to have any food on you, would you?"

"Well, how do you feel about cactus?" Derpy asked, producing some from a makeshift saddlebag and passing it to Twilight.

"Eh, better than nothing." Twilight replied, taking a bite out of the desert plant. After finishing, she said, "Come on. I know some of the ponies in Appleloosa; I'm sure they'll help us get back to Ponyville."

"Listen, Twilight. I'm sorry about what happened to your eye. I know what it's like to lose part of your sight." Derpy said, taking a more sombre tone.

"You had nothing to do with it, Derpy, and you saved my life. The main thing I feel for you right now is gratitude." Twilight replied, reassuring her friend and second in command. "I thought for the most part, you could see just fine."

"I can now, but I was born with a condition that nearly blinded me. It's not something I like to talk about, if you don't mind." Derpy explained.

Two Days Later

The two mares pressed on, tired and weary from two days of walking. Despite having plenty of daylight left, Twilight raised her front left hoof, motioning for Derpy to stop.

"What is it?" Derpy asked.

"Can't you hear that rumbling?" Twilight replied.

"You're right. It almost sounds like it's coming from ... below us!" As Derpy made that realization, she quickly pushed Twilight out of the way, and three massive tank-like vehicles drilled their way out of the ground.

The three tunnellers then formed a circle around the two mares, guns ready to fire. The lead tunneller's cockpit opened up, and a Diamond Dog climbed out. Twilight immediately recognized him as Rover, one of the Diamond Dogs who kidnapped Rarity a year and a half earlier.

"What do we have here? Ponies, and ones that have seen battle, no less. They will make excellent prisoners for Chief Boldheart," Rover commented. The cockpit on one of the other tunnellers opened up, this time revealing a bison.

"They don't look they're from Appleloosa. The one with the eyepatch is a unicorn, and the grey one's a pegasus," the bison pointed out.

"No matter, we take them anyway," Rover replied.

The back door on the last tunneller opened up, revealing two rifle-toting Diamond Dogs. They quickly ushered Twilight and Derpy into the tunneller, tying them to their seats, and making sure to bind Derpy's wings and cover Twilight's horn.

After the back door closed, Twilight and Derpy had to rely on guess work and their sense of hearing to figure out what was going on. It sounded as though the tunneller was moving, and had gone back underground.

About an hour later, the tunneller took a sharp and unexpected turn, slamming Twilight and Derpy's guards into the wall.

"Um, who's piloting this thing?" Derpy asked, but there was no response. After that, the background noise got a lot quieter, as if the vehicle had surfaced, or they had entered an existing tunnel. It was difficult to tell which it was without a window.

After a couple more hours, the tunneller stopped. "End of the line," Twilight commented, a resigned tone in her voice. However, when the back door opened, they weren't greeted by armed diamond dogs and bison, but by the ponies of Appleloosa.

"Get those two out of their restraints," Applejack's cousion Braeburn instructed, and two ponies entered the tunneller, freeing Twilight and Derpy, and then dragging the unconscious diamond dogs off.

Twilight approached Braeburn, and said, "Thanks. I thought the war hadn't made it this far yet."

"It hasn't, but as I'm sure you're already aware, Appleloosa's got its own problems," Braeburn explained, as Little Strongheart leaped out of the tunneller's cockpit.

"The bison aren't cooperating?" Twilight asked.

"Worse. The bison aren't cooperating with each other," Braeburn clarified.

"I heard them mention a Chief Boldheart, but I thought Thunderhooves was still leader of the bison tribe," Twilight commented.

"I am," Chief Thunderhooves stated, stepping out of the crowd of ponies and bison.

"Then who exactly is Boldheart?" Derpy asked.

"My brother. He disappeared three months ago, and when he returned, he was ... different. His coat was nearly black, and his eyes had an eerie green glow about them. It was unlike anything I had ever seen. He spoke of how bison had no stake in a pony war, and how the bison should sever ties with the Appleloosans. He was always deeply proud of his heritage, but he would never push the bison to civil war like this." Thunderhooves explained.

"You think the Changelings replaced him with one of their own?" Derpy suggested.

"No. An impostor would not look so flawed. If the Changelings are involved, they did something to him, but I'm sure it's him." Thunderhooves clarified.

"We should continue this discussion at the tavern; I'm sure our friends here could do with a stiff drink, after what they've been through." Braeburn then suggested, to nearly everyone's agreement.

The Salt Lick

Sitting down with a mug of ale in his hoof, Braeburn asked Twilight, "I thought Ponyville was Ground Zero for the Changeling attack; what are you two doing out here?"

"We were betrayed from within. The traitors killed the mayor and shot out my eye. Then, Queen Chrysalis hit me with a repulsion spell. If it hadn't been for Derpy, I'm sure I'd be feeding the buzzards right now." Twilight explained, taking a sip of her own ale.

"So Ponyville's fallen. I need to know, what's happened to my grandmother and my cousins?" Braeburn then asked, taking a more desperate tone.

"Granny Smith and Apple Bloom were evacuated well before the Changelings hit. As for Applejack and Big Macintosh, their gunship was still in the air, but that was almost a week ago." Twilight answered. "I can only hope they're alright."

"They will be. We Apples are survivors." Braeburn commented.

"I'm sure you understand that we need to get back to Ponyville as soon as possible; is there anything you could do to help?" Derpy asked.

"Normally, we run supplies out to Dodge Junction by train, but with the bison at each other's throats, they're needed more here, and it'd be a waste of fuel to send the two of you out with no cargo." Braeburn explained. "Unless you can somehow get the bison to resolve their differences, there's nothing I can do."

"Actually, I've been thinking about that. The Changelings tend to be proficient in mind-altering magic, and if they're manipulating Boldheart into turning the bison against each other, it wouldn't work if he knew of their involvement." Twilight said in response.

"You think they've erased part of his memory?" Thunderhooves asked.

"Exactly. If I can get close enough, I should be able to cast a memory spell on him." Twilight explained.

"Any supposed injustice inflicted by the Appleloosans would pale in comparison to the idea of being manipulated by the Changelings." Thunderhooves commented.

"The rogue bison have diamond dogs working with them and providing them with those tanks, and they're not going to be as easily persuaded. They've never seen eye to eye with the ponies of Equestria." Derpy pointed out.

"I know, but their tactics are opportunistic in nature, and we should have strength in numbers." Twilight replied. "If they don't run off, we should be able to subdue them relatively easily."

"It's risky, but it's better than a stalemate." Braeburn commented.

"I could use that tunneller I hijacked to get us into their underground stronghold, but they may already suspect I'm a double agent." Little Strongheart suggested.

"Good idea. It looks like Boldheart will be getting his pony prisoners after all." Twilight replied.

En Route To Rogue Bison Stronghold

"I really don't see why we need these bindings back on, even if they are loosened." Derpy commented, from the back of the tunneller.

"Passing ourselves off as prisoners is the only guaranteed way for us to get in." Twilight explained.

"How exactly does hoofing ourselves over to them help?" Derpy asked.

"My uncle makes a point of inspecting the prisoners personally; which will give Twilight the opportunity she needs to cast her spell on him." Strongheart answered from the cockpit.

"I can see this getting really violent if things get out of hoof." Derpy commented.

Rogue Bison Stronghold

Strongheart's tunneller arrived as Chief Boldheart was giving a speech to rally his troops. As she escorted Twilight and Derpy out, they just caught the tail end of it, and heard him say,

"My brother would drag us into a war led by ponies, to protect pony lands! But I ask you: Are we ponies, or are we bison?"

"WE ARE BISON! WE ARE BISON!" The crowd shouted in response, passionately stomping their hooves on the ground.

"Yes! We are bison, and we will not- I see my niece has finally returned, with the prisoners Rover promised. What kept you?" Boldheart continued, before spotting Strongheart enter the hall.

"I was waylaid by Appleloosans; my diamond dog comrades didn't make it." Strongheart explained, leading Twilight and Derpy up to the stage. In fairness, it wasn't exactly a lie.

"At least the prisoners are intact." Boldheart commented, before taking a closer look at Twilight and Derpy. "What happened to the unicorn's eye?" He asked.

"We don't know. She was like that when we found her." Rover pointed out. Then, Twilight found the opportunity she needed, and cast her memory spell through the fake horn sheath. Unfortunately, the spell was not as discrete as she had hoped, and the bright flash of violet energy quickly drew the attention of Chief Boldheart, the crowd of bison, and their Diamond Dog guards.

"Traitor!" Boldheart shouted, striking Twilight across the cheek. Motioning towards two armed diamond dogs, he said, "Throw my niece in with the rest of the prisoners."

As the diamond dogs led Twilight away, she thought to herself, It's over. I've failed.

However, her spirits lifted when she heard Boldheart continue his speech, and say, "We are bison, and we are pawns to no one! Not to the ponies, and certainly not the changelings! The cowards seek to rule us, and yet they dare not show their faces? They are the true enemy, and yet we bison fight each other while even ponies fight the changelings?"

"No! Changelings pay good gems for ponies! If you fight them, we fight you!" Rover shouted, raising his rifle, and motioning for the other diamond dogs to do the same.

"Bison! Attack!" Boldheart called out, the glow in his eyes fading and his coat returning to its natural brown. In the commotion, Derpy gave the guard escorting her a good buck in the gut, and slipped out of her wing bindings. Twilight then shot Derpy's guard with her horn, while giving her own a similar buck. With their guards subdued for the moment, Twilight looked out at the carnage. The bison had the advantage in numbers and sheer force, but the diamond dogs easily outgunned them at long range. It looked to be a stalemate. Between the pie-filled Battle of Appleloosa, the short Battle of Canterlot, and the two month long Siege of Ponyville, in which she was far from the front lines, this had to be the bloodiest battle she had ever been in.

Quickly thinking up a plan, Twilight said to Derpy, "I need you to fly back to Appleloosa as fast as you can. Tell Braeburn and Thunderhooves what's happened, and that the bison here need their help."

"But, Twilight-" Derpy was about to say.

"That's an order. Now go!" Twilight interrupted. Derpy then flew off, back out the tunnel they came in from.

Let's hope there's some bison left by the time they get here. Twilight thought to herself, readying her horn to fire upon the diamond dogs. While the diamond dogs could continue firing until their were trampled by bison or they ran out of ammo, Twilight was only limited by her own magical reserves. As she provided cover fire for the bison, she kept her eye out for Rover, the diamond dogs' apparent leader, but he was nowhere to be found, at least not in the main hall where the fighting was the thickest. Typical. She thought. Every shot she fired made it harder to maintain focus, and her lack of depth perception didn't help much either. First chance I get, I am reading up on Arcane Sight spells.

Appleloosa

Derpy finally arrived back in Appleloosa, her coat and mane drenched in sweat, and her wings completely worn out. As Derpy stopped a moment to catch her breath, Thunderhooves said, "You're back; did Twilight's spell work?"

"Yes, but the bison there need your help; the diamond dogs have turned on them." Derpy explained.

"Very well. Bison, move out!" Thunderhooves called out to the warriors of his tribe. Braeburn then motioned for Derpy to join in him in his gunship. While the gunships would be virtually useless inside the stronghold, they provided the ponies with the speed needed to get there in time.

Rogue Bison Stronghold

Twilight continued her barrage of hornfire, along with the occasional gun-jamming spell, but was beginning to feel the strain from the excessive magical exertion. Even with her above average magical abilities, it was becoming harder and harder to fight the urge to simply pass out.

You can rest. The cavalry will be here soon enough, and we've got the upper hoof. A voice kept nagging at the back of her mind.

No! You're the only one here who can fight the diamond dogs from a distance. Another voice retorted.

You're pushing yourself too hard. You can help without straining yourself so much. A third voice said, sounding the most reasonable so far.

For what it was worth, Twilight reduced the frequency of her shots, but she already felt like she was on the verge of collapsing, and eventually had to stop, suspecting one more shot would knock her out. Even that in mind, she felt she had no choice when she finally spotted Rover, his rifle aimed directly at Boldheart. She fired her last shot, just Rover fired his. She saw Strongheart push her uncle out of the way, and everything faded to black.

Appleloosa

Twilight woke up to once again see Derpy looking over her, but this time Braeburn was with her, and she was in a bed instead of on the ground.

"Did we win?" She asked.

"More or less. Rover is dead, and most of the surviving diamond dogs fled once we arrived. We have Boldheart's support, though he insisted on making the distinction that he and his followers would be fighting with us, and not for us. Unfortunately, Little Strongheart is in critical condition. It's hard to tell if she'll make it." Braeburn explained.

"I see. Is there anything else we can do to help?" Twilight asked, slipping out of the bed.

"Dodge Junction has far better medical facilities than Appleloosa. I'd feel a lot better about Strongheart's chances if you brought her there." Braeburn asked. "We can handle everything else here. If the Changelings make it this far, we'll be ready for them."

"Of course." Twilight replied. "We'll get her there safely. And thank you, for your help."

The Chapter With No Name

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En Route to Dodge Junction

The train ride provided Twilight and Derpy with a much needed respite, even if many of the ponies and bison on board were wounded being transported to Dodge Junction's hospital.

Seeing an opportunity to get to know Derpy better, Twilight asked, "So Derpy, how come I've heard so many ponies call you Ditzy Doo? Is that a nickname or something?"

"Actually, Ditzy's my twin sister. Mostly identical twin, but she tends to dye her mane and tail red." Derpy explained.

"So she's the one who dropped the ball on Bird Retrieval during Winter Wrap Up two years ago?" Twilight asked.

"Well, yeah. I was on Cloud Duty with Rainbow Dash." Derpy replied. "Listen, between Time Turner being stuck behind enemy lines, Dinky being alone in the Canterlot refugee camp, and Ditzy and Sparkler being deployed to Cloudsdale and Vanhoover, respectively, I don't really want to talk about my family right now."

"Believe it or not, Derpy, I know what you mean. I haven't heard a word from my parents, my brother, or my sister-in-law since the war started, and they're in Canterlot. Spike's practically my son, and he's trapped in Ponyville at the mercy of Queen Chrysalis." Twilight sadly replied.

"What about Cheerilee?" Derpy inquired.

"What do you mean?" Twilight asked, not quite sure what Derpy was talking about.

"Chrysalis tried to feed on you in her form; she must mean something to you." Derpy pointed out.

"She doesn't know." Was all Twilight said about it. That could have gone better. Twilight thought to herself.

As the train ground to a halt, medic ponies rushed aboard, ready to transport the wounded bison and ponies to the Dodge Junction Hospital. At the same time, one of the train's crew approached Twilight and Derpy, and said, "End of the line, ladies, unless you plan on just going back to Appleloosa."

"I thought this train went all the way to Ponyville, or at least Canterlot, considering." Derpy responded.

"Orders from Celestia. We're limited to two way trips to and from the nearest towns, for the sake of safety and security." The crew member explained.

Celestia? Luna is the one who should be making these decisions. Twilight thought, but said, "Is there anything you can do to help us?"

"There is another train going to Whitetrot, but that's about it." The crew member suggested.

"Thanks anyway." Twilight replied, finally getting up from her seat, and leaving the train with Derpy right behind her.

Dodge Junction

There was still a couple of hours before the train to Whitetrot arrived, so Twilight and Derpy saw no sense in just sitting at the train station the whole time, and wandered about the town, but their spirits further dampened at the sight of the refugee camps set up across Dodge Junction, much like the ones in Canterlot that they had heard about.

"Those orders from Celestia don't make any sense. It's inefficient, and way less secure. There's too much time wasted in transferring supplies from one train to another, and only going between the nearest towns is a huge waste of fuel. It would be like if when I had to deliver a package, I had to stop at the nearest house, pass it on to another mailmare, and she'd do the same, until it ended up where it needed to be." Derpy commented

"Celestia is supposed to be deferring to Luna in times of war anyway. None of this makes sense." Twilight pointed out.

"You don't think ..." Derpy tried to ask, but was afraid to finish the sentence.

Still, Twilight knew what she meant, and she answered with, "I'd rather not consider that. Even without the massive shield over the city, security in Canterlot has gotten a lot tighter. There are screeners everywhere, though they didn't seem to do much for Ponyville." Derpy couldn't help but notice a hint of self-flagellation at the mention of Ponyville.

"It's not your fault, Twilight. You couldn't have known they were going to betray us like that." Derpy said, trying to reassure Twilight.

"I should have suspected something! They were open to highest bidder, practically by their own admission, and all I did about it was reprimand them for attempted profiteering!" Twilight retorted.

"Ponies helping the Changelings was unprecedented, and we don't even know what Chrysalis offered them." Derpy pointed out. "Even if they hadn't betrayed us, Ponyville never was holding the entire horde back. There were reports of Changelings in Trottawa and Hoofington as little as a week after Ponyville was hit."

"I suppose you're right." Twilight conceded.

"For what it's worth, Twilight, I don't blame you. You're not the one who killed Mayor Mare, and you're certainly not the one who shot out your eye." Derpy said, finally managing to get through to Twilight.

"No, I'm not." Twilight replied, letting out a small smile. "Do you really think it'll be as easy as taking the train to Whitetrot?"

"Probably not. There aren't many towns that far north, but there are still plenty that are north of Canterlot." Derpy answered.

"Regardless, the sooner we get to Canterlot, the better." Twilight said in response.

Fortunately, their promenade had brought them close enough to train station to hear the sound of a train pulling in. The two mares ran to the train station as quickly as they could, but as they approached the front door, they were knocked back by an explosion that ripped the building apart. Twilight quickly got back on her hooves, having sustained little more than a few bruises and a nasty ringing sound in her ears. As soon as she spotted Derpy amid the chaos, she roused the grey pegasus and led her further into the wreckage.

Examining what was left of the two trains in the station, they quickly realized that casualties were light, due to the Whitetrot train primarily carrying supplies, and the Appleloosa train being vacant, except for the crew. While Derpy gave her aid to the medics rushing in, Twilight began further examining the blast itself, along with the cargo from Whitetrot.

"What exactly was the train from Whitetrot bringing here?" Derpy asked one of the medics.

"Ammunition and medical supplies, mostly. Nothing explosive, and certainly nothing strong enough to do this." The medic replied.

"I thought so. The centre of the blast appears to be in between the tracks, and there'd have been no time for a bomber to get a bomb into that spot before it went off." Twilight spoke up.

"Why wouldn't it have gone off sooner? There certainly would have been more casualties if it went off when we got here." Derpy commented.

"Think about it. Every dead pony is a pony the Changelings can't feed on. They want us alive and subdued." Twilight pointed out.

"Any idea how it was set up?" Derpy then asked.

"It's difficult to say. They could have rigged up something with pressure sensors, or the bomber could have had a remote detonator, but anything this close to the centre of the blast radius would have been incinerated." Twilight surmised.

"The bomber's probably posing as a pony who worked here, and they're probably still in town." Derpy suggested.

"Any sort of employee records would have been destroyed in the blast, but if they're a Changeling, they won't risk switching disguises; seeing two of a pony in town, or a complete stranger would be a dead giveaway." Twilight added.

"Maybe not. Places like this usually have some sort of safe in the main office, and it would have survived an explosion like this." Derpy pointed out. "Let's check there first."

As they entered the burned remains of the train station's main office, they found the safe already open, and a brown and red Earth pony mare going over a set of papers, somehow levitating them despite her lack of a horn. At the sight of Twilight and Derpy, she burned the pages, and threw them back into the safe. She then leaped out into the street, with the unicorn and pegasus mares quickly giving chase.

It would be easy enough for the bomber to get lost the crowd once she was in the open streets, so Derpy quickly flew up for a bird's eye view. Twilight then followed the bomber into the crowd, guided by Derpy from above. Once the bomber got out of the crowd, she took to the rooftops, seemingly propelled by invisible wings. Twilight turned towards the nearest alleyway, and started making her way up the wall, while Derpy swooped in on the bomber. The chase persisted across three more rooftops, until the bomber leaped out, and Twilight managed to shoot through one if her invisible wings. The bomber then tumbled to the ground, her pony disguise falling apart as she fell. Twilight jumped down after her, magically slowing her descent, and she and Derpy landed on opposite sides of the Changeling.

"Gotcha." Twilight said, trying to intimidate the Changeling. Not in the mood to surrender, the Changeling muttered something that sounded like little more than screeching and clicking noises to Twilight and Derpy, charged up its horn, and exploded.

Covered in green slime, Derpy commented, "I didn't know they could do that."

"Well, this has been an unequivocal disaster. Celestia seems to be deliberately sabotaging the war effort, we're stuck in Dodge Junction, and the Changelings have gotten deeper into Equestria than we thought." Twilight said in response. "Come on, I need a drink."

Dodge Junction Tavern

Having cleaned the bits of changeling off themselves, Twilight and Derpy entered the tavern, each ordering an ale. As the bartender poured their drinks, another mare entered the tavern and approached the bar, her face and mane obscured by a hooded cloak.

"What'll it be, miss?" The bartender asked the hooded stranger.

"Oh, um, just a Screwdriver. I mean, if it's not too much trouble." The hooded mare answered.

That voice was unmistakeable. Twilight turned to face this other mare, and asked, "Fluttershy?"

Escape from Ponyville

[youtube=_5lPqP62uxM]

Dodge Junction, Tavern

"Twilight! Derpy! You're alive!" Fluttershy exclaimed, her elation almost palpable as she embraced her friends in a group hug.

"It's good to see you too, Fluttershy," Derpy replied, trying to break free of Fluttershy's embrace.

"What are you doing out here?" Twilight asked. "What's happened in Ponyville?"

Glancing around for a moment, Fluttershy said, "It's a long story. We should find a table and talk about it." Fluttershy answered, getting up from her seat at the bar.

Ponyville, Two Weeks Earlier

Fluttershy flew as fast as she could to try to reach Rainbow Dash and her attack force, but stopped dead in her tracks as she saw a larger Changeling divebomb straight through Town Hall.

"No! Twilight!" She called out, and listened in horror as the voice of Queen Chrysalis came on over the town's PA system:

"I really must commend you all for your valiant efforts. I never thought ponies were capable of such violence. A shame it was all for nothing. Drop your shields, lay down your weapons, and welcome to Changelingville."

Fluttershy started to panic. She made her descent to ground level, but had little idea of how she could help now. Town Hall was lost, the town's defences were compromised, and the town itself would soon be overrun with Changelings.

Time Turner rushed out of the collapsing Town Hall, carefully avoiding the falling debris. With Derpy gone, his only thought was to get to the TARDIS, and get his stepdaughter out of the doomed town. We should have just sent her to Canterlot. Cheerilee would have taken good care of her. Once outside, he darted for the nearest back alley that looked like it would lead to the TARDIS.

Once he made it out into the open, the TARDIS was in sight, but as he approached, a Changeling landed in front of him, and as he tried to flee, two more landed on either side, and cornered him against a wall. All three Changelings then took the form of Derpy, their eyes glowing a malevolent green, and they began to feed.

Fluttershy's panic almost immediately gained focus when she heard a nearby stallion scream out in pain. When the sight of Time Turner being fed upon by three Changelings came into view, her training with Iron Will suddenly kicked in.

"You hurt my friend, you meet your end!" Fluttershy shouted, and in a fit of rage, snapped the neck of the middle changeling, bucked the right one in the face as hard as she could, and gave the left one the most intense Stare she had ever managed. Once that Changeling had flown away, and the other two lay dead at her hooves, she called out, "Time Turner!"

"Get me to the TARDIS. Call me Doctor." He said, sounding as though the feeding had taken a lot out of him.

"The what?" Fluttershy asked. None of the other feeding victims we found acted like this. She thought to herself.

"That!" The Doctor answered, pointing to a blue box across the square.

"Okay, Doctor." Fluttershy then flew him over to the blue box, but found herself unable to open it until he placed his left hoof on the door. Inside was a large orange-lit room, with six sided console in the middle of it. A little unicorn filly peeked out from behind the console, and fearfully asked, "Daddy?"

"Everything's going to be fine, Dinky." The Doctor said, getting free of Fluttershy, hobbling over to the console, and starting to operate it. The console started to make unnerving wheezing sound in response.

"Doctor, you're hurt. Let me help you." Fluttershy offered.

"No, I'm alright." The Doctor said, though it looked like he was struggling to stay on his hooves. "I knew this would happen eventually, and I was a coward not to face it sooner. Everything I've seen, everypony I've met, all the adventures, have made this one of the best lives I've ever lived." As he spoke, Fluttershy and Dinky could see a golden energy emanating from him, gradually building in intensity. "So this is how it ends. Fancy that. Just promise me one thing."

"Anything." Fluttershy replied, her eyes welling up with tears.

"Don't forget me." The Doctor said, and with that, he stood on his hind legs, stretched out his front legs, and let the energy explode out of him. Fluttershy instinctively shielded Dinky from the spectacle. Thankfully, he managed to avoid hitting the console, or any other important-looking piece of equipment. When the energy had dissipated, the Doctor, or at least the brown and chestnut stallion Fluttershy knew as Time Turner, was gone, and in his place was a wide-eyed black and grey Earth pony. The only thing to suggest he wasn't somepony else was that his cutie mark matched that of Time Turner, and he was wearing Time Turner's collar and green necktie.

"Okay, first things first. Mane: black and wavy. I like it. Coat: grey. Bit dull, but it works. Cutie mark: still an hourglass; why'd I think that would change? It's always been an hourglass." The Doctor said in a frantic tone, before running his hooves over his forehead.

"No! I'm still not a unicorn!" He added, sounding much more disappointed.

Then, recomposing himself, he asked, "Well, Dinky, Fluttershy, what do you think?"

"You look great, daddy!" Dinky replied, her excitement, and her relief that her stepfather was alright evident in her tone.

"Um, what just happened?" Fluttershy asked, still confused by the whole spectacle.

"Come on Fluttershy, you're acting like you've never seen a Time Pony regenerate before." The Doctor said

"Well, I haven't." Fluttershy said in response.

"Right. You're not Derpy. Now I remember why I explained all of this to her and the fillies in advance." The Doctor muttered under his breath. "I'm not a normal pony like you, I'm a Time Pony."

"You look like an Earth Pony." Fluttershy pointed out.

"And I could look like a Unicorn or a Pegasus, but I'd still be a Time Pony. When we're about to die, we can heal ourselves, but in doing so, every part of us changes, like you just saw." The Doctor explained. "I'd be dead if you hadn't intervened. Thank you."

Instead of responding as the Doctor had expected, Fluttershy finally realized what she had done to save him, and started to hyperventilate. "I killed them, with my own hooves." She said quietly, starting to cry.

"I don't like killing any more than you do, Fluttershy, but I owe you my life. We wouldn't have made it out if you hadn't." The Doctor said, trying to reassure her.

"Made it out?" Fluttershy asked, confused by the statement.

"Just before I regenerated, I set the TARDIS to leave Ponyville." The Doctor explained.

"You can't just leave everypony down there!" Fluttershy shouted.

"I'm not abandoning them; they can't win this fight without help, and they need more help that I alone can offer them." The Doctor retorted.

"Alright. Where are we going? Canterlot?" Fluttershy asked.

"No. By the time we get there, they'll already know what's happened to Ponyville." The Doctor replied.

"Then where are we going?" Fluttershy then asked.

"East. If Twilight and Derpy are alive, that's where they'll be." The Doctor answered.

"And ... if they're not?" Fluttershy asked, not wanting to consider the possibility.

"I don't know. It's a gamble, but it's the best plan I can come up with on short notice, especially just after regenerating." The Doctor said.

Dodge Junction
Present

"We've been looking for you two ever since." Fluttershy explained, leading Twilight and Derpy out of the tavern. Waiting outside for them was something Derpy feared she would never see again: The TARDIS. Next to it was the stallion Fluttershy claimed Time Turner had regenerated into, but he was wearing a light blue bow tie instead of Time Turner's necktie, along with a black top hat. The Doctor had told her, and her daughters, all about regeneration, and Fluttershy told her it had happened, but seeing his new form for the first time was difficult, especially since she did not see him regenerate.

"Doctor? Is it really you?" She asked, feeling that the name Time Turner no longer suited him.

"It's good to see again, Derpy, even if it is through a new pair of eyes." The Doctor answered.

"I should have been there." Derpy said, tearing up at thought of what the experience must have been like for Dinky. For most of the little filly's life, Time Turner had been closest thing she had to a father.

"You're here now, that's what matters." The Doctor replied, embracing his wife closely.

"How is Dinky handling it?" Derpy asked.

"Pretty well, actually." The Doctor replied. The TARDIS door then opened via unicorn magic, and Dinky ran out, shouted, "Mommy!", and embraced her mother and stepfather in a big hug. Twilight and Fluttershy decided to give them all a moment, but still smiled at the happy reunion.

Maybe there is hope in this war after all. Twilight thought to herself.

Number 8

[youtube=_5lPqP62uxM]

The TARDIS

Dinky wandered the halls of the TARDIS, occasionally listening in on some of the conversations in the main console room. Sometimes it seemed like the one-eyed mare was just looking for reasons to argue with everypony else.

"Fluttershy, you must have killed dozens of Changelings from your turret; what was so different about those two?" She heard the one-eyed mare ask the pegasus who had saved her stepfather.

"It's not the same, Twilight, when I was shooting them down, I could detach myself from it, and not think about it. When I killed those two, I felt them die." Fluttershy answered. "That's not something anypony can just shrug off."

"But it is something you're going to have to learn live with." The Doctor said, putting his right foreleg around Fluttershy. "Twilight, you're not helping here; she's been through enough without you questioning her about it."

Twilight lowered her head in shame, and said, "I'm sorry, Fluttershy. I'll go."

Fluttershy was particularly sensitive, and being driven to an act of brutality like that wouldn't sit well with any pony. It was surprising that she was taking it as well as she was. She was about to turn and leave, when the Doctor said, "Wait, there's something I wanted to talk to you and Derpy about."

"What's is it?" Twilight asked.

"I want to know what happened in the War Room, when Chrysalis got there." The Doctor inquired in response.

"I don't know how much help I can be with that; I was still in shock from losing my eye, and I lost consciousness soon after." Twilight explained. "When I woke up, Derpy and I were about a four-day walk away from Appleloosa."

"That far?" The Doctor commented.

"It would have been farther, if Derpy hadn't used her wings to slow us down." Twilight elaborated.

"Fascinating. As powerful as she is, there's no way Chrysalis could have launched the two of you that far." The Doctor pointed out.

"She couldn't have fed on anypony for more power; my pain protected me, and she didn't try feeding on anypony else in the War Room; Mayor Mare was already dead, Flim and Flam were on her side, and Derpy evaded her attention." Twilight added. "Maybe she had just fed on some prisoners before she hit Town Hall."

"Maybe, but it would have taken a lot of feeding to make her that powerful." The Doctor pointed out.

"There seems to be a lot going on right now that just doesn't add up. I've been close to Princess Celestia since I was a filly, but I can't begin to explain the decisions she's made regarding the war effort; decisions that should be in Luna's hooves anyway." Twilight commented.

"I don't like the sound of it any more than you do, but there's not much we can do about it until we reach Canterlot. In the meantime, you should try to get some sleep. You look like hell, Twilight." The Doctor instructed. "I'll let you know when we get close."

Grumbling, Twilight walked out of the console room, and started to navigate the labyrinthine halls of the Doctor's strange vehicle, finding its dimensions fascinating. Not even Starswirl the Bearded could figure out figure out how to make things bigger on the inside like this. Passing by Dinky and Derpy, she entered the quarters the Doctor had set up for her. For everything the TARDIS was capable of, the quarters seemed rather spartan. There wasn't much there, other than a rough looking bed, and an end table with a lamp on top. Twilight slipped into the bed, and thought, It's not the best, but at least it beats sleeping on gravel.

Twilight awoke to find the bed much more comfortable than it was when she went to sleep. Looking around, the room she woke up in looked nothing like her quarters in the TARDIS. In fact, it looked very much like her bedroom in the Ponyville Library. She got up, and looked out the window, to see Ponyville, with no sign of the militarization she had instituted, or the damage caused by the Changelings' attacks. Then, she caught a glimpse of her reflection, and instead of seeing the burned mess covered by an eye patch she had grown accustomed to, she saw her right eye, perfectly intact. Instinctively, she turned her head around, and called out, "Spike?" No response. However, she did notice the number 8, plastered over her cutie mark in black, and she quickly checked her other flank to find it there as well.

"What is going on here?" Twilight asked out loud, not expecting a response. She trotted down the stairs to the main section of the library, hoping to find some explanation for her present circumstances. When she made it to the ground floor, she immediately noticed a book off the shelf, just sitting on the table in the middle of the room. Normally, she'd just put it back on the shelf without much thought, but due to the present circumstances, she instead decided to look it over thoroughly. The first thing she noticed was that the text on the cover was actually just a collection of odd symbols that resembled Equish text, and that even the words they looked like were pure gibberish. She then opened the book, only to find horizontal black lines in place of text. Confused, she pulled several books off the shelf to examine them, and found the same oddity in them as well.

Then, Twilight heard a knock on the front door, and quickly ran over to open it. On the other side was Derpy, wearing a saddlebag, full of muffins on the left side, and three books on the right.

"Hey, Twilight! I'm just here to return these books I took out for Dinky last week." The mailmare said.

"Um, what happened to the TARDIS, and how did I get my eye back?" Twilight asked, magically removing the books from Derpy's saddlebag.

"The what? I didn't know you lost it. Your eyes look fine to me." Derpy responded, confused by Twilight's bizarre question. As Derpy entered the library, Twilight couldn't help but notice a number 7 over the wall-eyed pegasus's bubbly cutie mark.

"You know, your husband's freaky blue box thing?" Twilight added, trying to jog Derpy's memory.

"I don't know what you're talking about, Twilight. You know Time Turner is just a clockmaker. Now, can we hurry this up? I still have packages to deliver, and I have to pick up Dinky from school." Derpy retorted, starting to get annoyed

"Pick her up from school? It's only eight in the morning." Twilight said, pointing to a clock on her wall, showing that it was 8:00.

"No, it's half past three in the afternoon." Derpy replied, pointing to the same clock, now showing that it was actually 3:30.

Though she was confused by this, Twilight set the books down on her desk, and marked them down as returned.

"Thanks, Twilight. Be seeing you!" Derpy said, about to fly off, before Twilight asked, "Wait. Derpy, do you know anything about the numbers over our cutie marks?"

"I'm Number Seven, and you're Number Eight." Derpy answered.

"Who's Number One then?" Twilight inquired.

"Here, have a muffin. I think you need one." Derpy then pulled a muffin out of her bag and hoofed it to Twilight. She then flew off, once again leaving Twilight alone. Twilight was just as confused as before about her present circumstances, and she quickly decided that staying in the library would do little to remedy that situation.

"If anypony knows what's going on here, it'll be Pinkie Pie." Twilight thought out loud as she stepped outside. She couldn't help but notice the absence of other ponies in the vicinity. The library wasn't exactly in a busy part of Ponyville, but it was never this empty.

"Where is everypony?" She asked out loud, doubting she'd get a straight answer. After an uncharacteristically short walk to Sugarcube Corner, she heard the tune of "For She's A Jolly Good Filly" inside. Entering, she found one of Pinkie Pie's signature parties, but something seemed off. To begin with, the Cakes, Pinkie Pie's employers and landlords, were nowhere to be seen, nor was anypony other than her close friends, and each of them had a number on their flanks as well, ranging from Six to Two. In addition, there was little in the way of party supplies, except for anything currently in use by one of her friends.

Seeing Twilight enter, Pinkie approached, and said, "I'm so glad you could make it, Number Eight. We've been wondering when you'd show up."

Quickly checking Pinkie's flank, Twilight said, "Thanks, um, Number Four. What's the occasion, anyway?"

"Oh, it was Number One's idea. She said you were under a lot of stress, and you needed something to help you unwind." Pinkie Pie explained.

So, Number One is a mare. That'll help narrow it down. Twilight thought. Then, she asked, "And who is Number One, anyway?"

In response, all of her friends started laughing. "Can you believe Number Eight here? She doesn't know who Number One is!" Rainbow Dash, marked as Number Two, said. "That's a good one, sugarcube." Applejack, marked as Number Three, remarked.

"I'm serious! Who is Number One?" Twilight shouted, but it did little to stop their laughter. Frustrated, she charged up her horn, and ended up shooting a hole in the ceiling. After the dust cleared, all of her friends were gone, except for Fluttershy, marked as Number Six.

"I'm sorry, Twilight. I can't tell you who Number One is, but I can tell you where she is." Fluttershy said to her.

"Then where is she?" Twilight asked.

"Town Hall-" Fluttershy was about to say more, but Twilight had bolted the moment she knew where to go. Still, she let out a quiet, "Be seeing you." anyway.

Twilight ran to the Town Hall as quickly as she could, but upon her arrival, she found the interior to be vastly different from how she remembered. In place of the bright lighting and the high ceiling, she found a dark corridor, sporadically lit from a low ceiling. At the end of the corridor was a double door, leading into a small office, and sitting at the desk was none other than Princess Celestia, typing away at a typewriter on her left, and drinking a cup of tea on her right.

"Princess Celestia? I should have known you'd be Number One." Twilight said.

"I am not Number One, Number Eight. I am not part of the system, and therefore have no Number. You abandoned and alienated your friends, all in the name of your obsession with Number One. Was it worth it, Number Eight?" Celestia asked.

"Enough with the Numbers! My name is Twilight Sparkle, and I will not be pushed, filed, stamped, indexed, briefed, debriefed, or numbered! My life is my own!" Twilight shouted, slamming her hoof down on Celestia's desk, and breaking the saucer under her tea cup. At that point, the typewriter released the page it was typing onto, and the page fell onto the desk. Upon a quick examination, Twilight saw that it was actually a photograph of her, and Celestia had crossed it out with the typewriter's 'X' key.

"We'll see about that, Number Eight. Be seeing you!" Celestia replied, and Twilight started to hear the sound of machinery from above. She looked up to see that the office's ceiling was gone, just as a large mechanical claw reached down and grabbed her. It then pulled her up and out of the office, revealing a massive hall of gigantic filing cabinets. Off in the distance, she saw a drawer open as if it was expecting her. Twilight was terrified, knowing she was powerless to escape, and fearing what else might be in that drawer. She struggled to break free, but to no avail. The claw then stopped over the open drawer, and let Twilight fall in. As she fell, she saw only darkness inside the drawer, and focused on the light from outside, but lost even that as the drawer closed on her.

"This has gone on long enough! Tell me! Who is Number One?!" Twilight shouted, in a combination of panic and anger. In response, a light seemed to turn on above her, revealing a window, with Chrysalis looking at her through it.

"I am Number One! I am everything you despise. Your hatred for me drives you, gives you focus. You are nothing without me!" Chrysalis answered.

"No!" Twilight responded, raising a hoof to the window, but then she discovered to her horror that it wasn't a window she was looking at Chrysalis through; it was a mirror. She was Chrysalis.

"I twist everything to my will, but you, I'm particularly proud of. All I had to do was make you aware of me, and you did the rest." Chrysalis explained, practically taunting Twilight.

"NO!" Chrysalis/Twilight charged up her horn, and shot the mirror. While it did not break, the reflection changed, and she changed with it. She was once again the grizzled, one-eyed soldier that the war with the Changelings had made her into.

"I am Number One. I am the soldier who destroyed Ponyville in order to save it, and failed." Her reflection said to her.

"You're wrong! Chrysalis destroyed Ponyville!" Twilight tried to counter.

"Did she? You took an idyllic farming village, and turned it into a warzone. You destroyed Ponyville well before any Changeling set hoof there." Her reflection explained.

"I did what I had to do!" Twilight shouted at her reflection.

"You tell yourself that every night, but you don't believe it." Her reflection said in response.

Not wanting to hear any more, Twilight shot the mirror again, and this time it shattered. However, behind it was another Twilight, naked and with both eyes intact, who said, "I am Number One. I am everything you claim to be fighting for, but at what cost?" The second Twilight asked. Then, pointing to her right eye, she said, "Do you think this will just grow back?"

"No, of course not." Twilight answered.

"There is no going back. Be seeing you." The second Twilight then produced a small white ball, and threw at the first. As it approached, it expanded, becoming large enough to contain an adult pony. Once it reached Twilight, it took on a more malleable consistency, and then simply enveloped her.

Twilight awoke in a cold sweat, back in her quarters in the TARDIS. I must have just been dreamt all of that. She thought. She then ran back to the console room, to find the rest of the group waiting there. "Twilight! I was just about to call you. We're within range of Canterlot, and we should be there in a few minutes." The Doctor said, still hard at work on the controls.

"Good. Celestia, we need to talk." Twilight replied. Then, with a smile on her face, she added, "Be seeing you."

Trust No Pony

Canterlot

The TARDIS materialized in a back alley in Canterlot, and as the travellers stepped out, they soon saw that while no Changelings had set hoof there since the Battle of Canterlot, the war had certainly taken its toll on the capital. Gone was the city's regal splendour, replaced with an air of gloom and dread. Guards were patrolling most of the streets, and shanty towns, brimming with refugees, seemed to have sprung up everywhere. Huge gun turrets had been mounted on the tallest buildings, and all along the outer walls. Even the sky did little to ease the gloomy mood of the place; the skies were almost always clear above Canterlot, but they were overcast now.

"Doctor, why did you park the TARDIS here? We could have materialized right in the middle of the War Room." Twilight asked the Doctor, as they entered a main street.

"You and Derpy have spent most of the war so far in Ponyville's War Room, Twilight. It's easy to lose perspective in there." The Doctor explained.

"You picked a hell of a way to rectify that. Ponyville is my home, but I was born and raised here, and I never wanted to see it like this." Twilight said. She shuddered to think of what Ponyville looked like now.

"Celestia only knows what's become of Ponyville." Derpy commented. Fluttershy, however, remained silent, seemingly taking in the sights of wartime Canterlot.

Part of Twilight wanted to see her parents, or all the ponies who had been evacuated from Ponyville, but she knew how important it was that they get to the palace.

After a while of walking, Fluttershy said, "Um, is it just me, or do all the guards have their eyes on us?"

Everypony in the group then looked around, seeing that Fluttershy was right. "New arrivals must be rare." Twilight commented.

"At the very least, they should recognise us, Twilight." Derpy pointed out. The Doctor then noticed that the guards were readying their spears. "Something's wrong." He said. He then directed them into another back alley, just as a guard chucked his spear at them.

"That was hardly the welcome I was expecting." Twilight commented.

"I don't understand. Why would they just start throwing spears at us? They know who we are." Fluttershy asked.

"Celestia's orders. Why else?" Twilight surmised, dodging another spear.

"Come on! We need to keep moving!" Derpy shouted. The group then took a sharp right, just as another spear lodged itself in the wall.

"We should split up; we'll do no good if we're all caught!" The Doctor called out. Derpy grabbed Dinky in her forelegs, and then she and Fluttershy flew up to the rooftops, leaving Twilight and the Doctor to find alternative ways up. Losing sight of the Doctor, Twilight ran inside one of the buildings, caring little for her surroundings, except for what might work as roof access. Carefully navigating through what looked like a restaurant's kitchen, she spotted a stairwell and made her way up, hearing several sets of hooves behind her. Once she reached the room, she exited the building, and shut the door, fusing the hinges shut with her horn. That'll buy me a bit more time. She thought.

Twilight then started looking around for the closest rooftop to jump to, hearing the guards making their way up the stairs. Of course, this was nothing like chasing that Changeling in Dodge Junction; there, it was a simple matter of chasing the bomber in a straight line over flat rooftops with relatively uniform height, and here, she was the one being chased, with no clear direction, and Canterlot's skyline was far more diverse than that of Dodge Junction. Aware that she had little time to think, Twilight then made the leap to the nearest building, missing, but still managing to reach an exterior stairwell. Unfortunately, this building did not have a direct form of access to the roof, and it was too steep to walk on anyway. Making do, Twilight made her way to the top of the stairs, and entered the building from there, hoping to find another relatively safe jump on the other side. Luckily, the neighbouring building was close enough that she managed to land safely on its roof.

Twilight managed to keep it up for another ten rooftops, but then she found herself cornered on a balcony, with no safe path to the nearest rooftop, nor anything on the side of the building, save for some closed windows. Hearing the guards hoofsteps, Twilight took a deep breath and leaped off the balcony, aiming for the closest of the closed windows.

Surrounded by broken glass, Twilight slowly got back up on her hooves, and realized exactly where she had landed. This had been her bedroom when she was a filly. In midst of all that running and jumping, she must have lost track of where she was. Twilight started to look around at her old room, when she heard two sets of hooves approaching the door. Still in a panic, she charged up her horn, expecting guards behind the door, but instead, her mother and father knocked the door open, holding a baseball bat and a frying pan in their horns, respectively. At the sight of their daughter, both of them dropped their makeshift weapons, and started to tear up. Conversely, Twilight let the energy in her horn dissipate, and said, with tears forming in her eye as well, "Mom? Dad?"

The three of them then embraced in a group hug, and Twilight's mother, Twilight Velvet, said, "We thought you had been killed."

"I'm alright." Twilight said, trying to reassure her parents.

"What happened to your eye?" Her father, Crescent Sparkle asked.

Twilight took a deep breath. She didn't want to worry her parents, but she didn't want to lie to them either. "I got shot." She finally said, taking off her eye patch.

Twilight Velvet gasped, but then said, "No matter what scars you bear, you're still our daughter."

"What brought you back to Canterlot?" Crescent Sparkle inquired.

"Well, even if I'm not dead, I was still taken out of the picture, where Ponyville was concerned. I ended up outside Appleloosa. When I got here, the guards just attacked me on sight." Twilight explained.

"They said they were on the lookout for a terrorist who bombed Dodge Junction's train station." Crescent Sparkle suggested.

"I was there, but I caught the real bomber, before it committed suicide, at least." Twilight reassured them. "I don't know why they'd think I did it."

"You know we believe you." Twilight Velvet answered. Then, they all heard a heavy banging on the door.

Twilight took a deep breath. "I've got nowhere to run this time."

"Do what you have to. And don't forget we're proud of you." Crescent Sparkle said, patting Twilight on the back. Twilight gave her parents one final look, and let a single tear fall from her eye, before leaving her bedroom. She watched as the guards broke the front door down, and approached her. However, instead of simply escorting her out as she expected, one them clubbed her with his hoof, rendering her unconscious, and they dragged her out of the house.

Canterlot, Prison

Twilight awoke to find herself in a cell within the Canterlot prison, with no sign of the rest of her party. I was once the personal protegé of Princess Celestia. How is this my life? She thought to herself, before hearing noises from beyond the door.

"Sister, I must protest! Twilight Sparkle is a soldier under my command. She is my responsibility." Twilight heard Luna say from beyond her view.

"I don't care who you are. I will not have you using guards under my command to arrest my sister and assault my parents without informing me." She then heard her brother's voice, and both he and Luna entered the wing of the prison, accompanied by Princess Celestia, the doors opening with an uncharacteristically green glow from Celestia's horn.

"Twilight Sparkle, my greatest student, and my greatest disappointment. First you abandon your post, and then you bomb a train station? Oh how far you've fallen." Celestia said in a contemptuous tone.

"If I was behind the bombing in Dodge Junction, why would I come back here, straight to the palace?" Twilight asked.

"Your next target, obviously." Celestia said.

"With what? Your own guards gave me a thorough search, and they didn't find any explosives on me. And if I was going to bomb the palace, I think I'd do something a little smarter than going for the front door, without any explosives on me. And where's Derpy, Fluttershy, and the Doctor?" Twilight then asked, finding her mentor's accusations increasingly absurd.

"Your accomplices are being dealt with elsewhere." Celestia answered.

"Accomplices? I recruited Miss Hooves myself." Luna interjected.

"Perhaps you should have taken more care about who you recruited, sister. Unless you're part of this as well." Celestia then accused Luna.

"I am the Princess of the Night! It is my duty to lead Equestria in times of war!" Luna retorted.

Though she had her suspicions about the Princess, that exchange removed all doubt in Twilight's mind.

"You are not Princess Celestia." She accused the so-called Princess of the Day.

"You stand in a prison cell, and you accuse me of being a Changeling?" Celestia asked in return.

"Twily, that's impossible. Celestia must gone through the screeners dozens of-" Shining Armour stopped there; he couldn't actually think of a single instance of Celestia going through a screener.

"We need a screener in here. Now." He then said to the guards by the door. The two guards then ran out of the room to retrieve one.

"I didn't say you were a Changeling. Celestia would have listened to my side of the story before having me arrested. She also wouldn't have have superseded her sister's authority, or my brother's, like you did." Twilight explained.

"War changes ponies." Celestia countered, starting to panic.

"I know that just as well as you do, but one thing that shouldn't change is the colour of your magic; it should be golden, but it's green." Twilight added.

Celestia grinned wickedly, and then said with a male voice, "Fine, you've got me."

Crouching Pony, Hidden Changeling

Canterlot, Prison

Celestia's form vanished in a green flame, and in her place was a male Changeling, rivalling Chrysalis in stature.

"I see my charade is at an end. A pity." He said with a sinister grin on his face. Just as the two guards returned with an active screener, Shining Armour grabbed it and threw it at the Changeling, while Luna freed Twilight from her cell. Unfortunately, the Changeling managed to shoot the device down before its threshold crossed him. It lay smouldering at his hooves.

"I have been feeding on every single pony's love for Celestia. Do you really think a simple screener is enough to stop me?" He taunted them.

"No, but I'm not the one foolish enough to remove my disguise inside a prison." Shining Armour retorted.

"No prison can hold me." The Changeling then lunged at the stallion, with his teeth bared and his horn charged and ready to fire. Shining Armour then raised a shield over himself, Twilight and Luna, while Twilight took the opportunity to shoot out the Changeling's right wing. The Changeling crashed into the wall on his right, but quickly got back on his hooves. He prepared to release an explosive blast from his horn, but additional guards rushed in from both sides of the cell block. Just before he was able to cast the spell, one of the guards behind him speared him in the right hind leg. The Changeling then fell to the floor, no longer able to put up a fight.

Some Time Later

Once Celestia's imposter had been subdued, he had been placed in the most secure cell in the prison, and the guards had been sure to bind his wings, and place a magic-inhibiting sheath over his horn. Twilight, Luna, and Shining Armour, now joined by Cadance and the Doctor, approached the Changeling's cell.

"State your name, rank, and intention." Luna said, her tone suggesting a deeply suppressed anger towards the Changeling.

"Larva, Prince, Sabotage." The Changeling, apparently known as Prince Larva, answered.

"How long have you been posing at the Princess?" Shining Armour then asked.

"I'll never tell." Larva responded with a smug grin on his face.

"Where is Princess Celestia?" Twilight inquired, doing little to conceal her own anger.

"She was such a feast!" Larva taunted them.

"Chrysalis had the perfect opportunity to kill me. Why didn't she?" Twilight demanded.

"She did far worse than kill you. Look at what you've become, Commander. She hurt you, and she's going to keep on hurting you. When all of Equestria is ashes, you will have her permission to die." Larva continued to taunt her.

This was enough to push Twilight over the edge. She charged up her horn, and lunged at the cell, "Are you going to talk, or just make vague threats? Unless you tell us something useful right now-" Twilight threatened, before Cadance pulled her away.

"What in Equestria do you think you're doing?" She asked, horrified by how vicious her sister in law had become.

"We're done here anyway." Luna interjected, and led the group out of the cell block.

Just outside, Luna asked, "Doctor?"

"There was definitely some form of psychic interference affecting Larva, although it's impossible for me to say to what extent or for what purpose." The Doctor explained.

"I want you to compare it with some of our Changeling captives." Luna instructed. "We'll reconvene in the War Room in one hour."

While most of the group left, Cadance remained, after spotting Twilight just sitting at the wall.

"Talk to me, Twilight. You haven't exactly been acting like yourself lately." She inquired.

"It's been a rough three months. Your mother tasked me with holding the Changelings back at Ponyville, and I blew it. Two months of pain and horror for nothing." Twilight explained.

"For a lot of ponies, those two months made all the difference in the world. My mother wasn't mistaken in recruiting you. You never let her sister down either." Cadance tried to reassure her, but Twilight turned away at the mention of Celestia.

"I'm sorry. I miss her too." Cadance added.

"We all do. The hardest part is that we don't even know when they took her. It's like you marrying my brother is the one thing that's gone right since the Battle of Canterlot." Twilight remarked.

At that point, something clicked in Cadance's head, "The Battle of Canterlot? I need a word with my mother." Cadance took Twilight by the hoof, and led her back to the War Room.

War Room

Twilight and Cadance entered the War Room to find the Doctor and Luna discussing the revelation within the prison.

"First my daughter, now my sister. And this time I don't think we'll be getting her back." Luna remarked.

"At least you got your daughter back, and I have to hoof it to the Changelings. It was an excellent ploy." The Doctor commented.

"A ploy?" Twilight inquired.

"Think about it. As long as Larva was posing as Celestia, he was free to sabotage our war effort as he saw fit, and once he was exposed, pony morale went down the drain." The Doctor elaborated.

"You say that like you knew all along." Twilight surmised.

The Doctor said nothing, but he gave Twilight a look which confirmed her suspicions.

"How could you have known?!" Twilight demanded.

"My vehicle, the TARDIS, travels in time as well as space. I've been to the future, I've seen Luna ruling alone from her palace in Ponyville." The Doctor admitted.

"You could have done something!" Twilight shouted.

"Like what? I knew they replaced her, but I never knew when or how. I've travelled in time, and I've been to your future, but that doesn't mean I know everything. I didn't even know they were going to get me when they did." The Doctor retorted.

Before the argument between Twilight and the Doctor could get worse, Cadance piped in and said, "Mother, I think I know when they took Celestia. When they attacked Canterlot, they trapped her in some sort of cocoon thing, and there was a bright flash of energy when it was sealed."

"That would have been the perfect opportunity to conceal a teleport." The Doctor commented. "But why bother? The Changelings had practically won at that point, and everything else about Chrysalis's behaviour suggested she wasn't expecting to be driven out of the city."

"The slow blade penetrates the shield." Shining Armour said as he entered the War Room. "Chrysalis knew just as well as we did, that no matter who won the Battle of Canterlot, it was only the beginning. She's far smarter than we've been giving her credit for."

"How exactly does knowing when they took Celestia help us? Nothing changes the fact that we have no leads on where she is now." Derpy pointed out.

"Actually, Derpy, it does explain how Chrysalis was able to launch us so far." Twilight reminded her. "The fact that the Changelings have Celestia in their hooves tells us the kind of power they wield."

"There's something else you need to see, Twily." Shining Armour then pulled up an image on the main screen. It appeared to be a massive green sphere, just outside the Everfree Forest. A quick examination suggested it was a shield like the one Shining Armour put up over Canterlot, except it was completely opaque.

"What is that?" Twilight asked, not identifying the surrounding landscape.

"Ponyville. That appeared a month ago, just after we lost contact with you." Shining explained. "The fact that they haven't done this anywhere else suggests a considerable strategic value for it."

"Have you tried breaching it?" Twilight asked.

"Yes, and nothing so far has worked. I suspect it would take the combined strength of my sister and I, or the Elements of Harmony to do it." Luna added.

"Celestia's gone, and we'd have to either get the rest of the bearers out of there first for the Elements of Harmony to work. or get Fluttershy and I in there with the Elements themselves and take it down from the inside." Twilight pointed out. "Which will it be?"

"If Chrysalis has been feeding on Celestia, then we don't have the firepower to take her on after destroying that barrier. There's nothing we can do for now." Luna stated. "We also need time to undo Larva's sabotage."

"I don't like it, but I guess we have no real choice." Twilight said in response.

Six Months Later

Over the next six months, Twilight worked extensively to prepare for the return to Ponyville, coordinating with Luna on the planning the attack, as well as fine tuning her skills in both ranged and melee combat. At the first opportunity, she had tracked down Cheerilee in the city, and made her feelings known, only to have them rebuffed, as Cheerilee had no interest in other mares. However, Twilight soon found herself in a relationship with a journalist, an Earth stallion by the name of Keen Eye, with whom Luna assigned her to work on softening the blow of losing Celestia for the general population. When she could, she spent time in the Canterlot Archives, researching magical countermeasures against the Changelings, along with spells that had the potential to effectively restore her sight.

Canterlot Archives

"Twily, you wanted to see me?" Shining Armour asked as he entered the room, noting the dim lighting and the presence of a spellbook, and Twilight's eyepatch on a table.

"Yes. I'm glad you're here." Twilight answered, stepping out of the shadows. For a moment, Shining was taken aback; it was the first time he had seen his sister without her eyepatch since her return to Canterlot.

"Are you having trouble with your research?" Shining inquired. He was used to her coming to him for help in her military work, but not with work like this. This was her area of expertise.

"No, well, yes. I've finally found a spell that should restore my eyesight, but because of how it works, it's impossible for me to cast it on myself." Twilight explained.

"You're found a way to grow your eye back?" Shining was cautiously optimistic.

"Not exactly. It's called Arcane Sight. It allows a pony to see through an inanimate object. If it were cast on my eyepatch, it would be like I had two working eyes again." Twilight elaborated. Shining then examined the spell in the book.

"This looks like one of the most exhausting spells I've ever seen. I think you'd have a better chance of it working if you asked Captain Lulamoon-" Shining Armour was about to say.

"Captain Lulamoon was killed in Trottingham two weeks ago, along with the rest of Great and Powerful Company." Twilight pointed out.

"Alright, let's do this." Shining then charged up his horn with great difficulty, and fired the first half of the spell at his sister's eyepatch. He had to stop a moment to catch his breath, but he started on the second half as soon as he could. after he cast it, he felt like passing out, but he noticed how confused and disoriented his sister looked, so he grabbed her eyepatch with his horn, and placed it back on her.

"It worked!" Twilight shouted, hugging her brother in thanks.

"We should be getting to the War Room. It's almost time." Shining said, still breathing heavily.

"Let me say goodbye to Mom and Dad, and Keen, and I'll be right there." Twilight replied, and the two left the archives together.

War Room

The two siblings entered the War Room to find the TARDIS parked under the main screen, and the meeting was in full swing.

"The Doctor's TARDIS will bypass the Changelings' barrier, and get the four of you in there. After that, it's just a matter of finding the other Element bearers, and then using the Elements to take down the barrier." Luna explained.

"It almost sounds easy when you put it like that." Twilight commented.

"We'll begin our attack as soon as the barrier is down." Shining Armour added, but he noticed how uneasy Fluttershy was, and asked her, "Fluttershy? Is something wrong?"

"I'm a killer. How can I be the Element of Kindness anymore?" Fluttershy asked, not directing the question at anypony in particular.

"You're still kind. You did something that went against everything you were, but you didn't let it change you." Cadance said to reassure the timid Pegasus. Fluttershy nodded in response.

"If everypony is ready..." She then tried to ask. The Doctor and Derpy nodded, and entered the TARDIS, with Fluttershy quickly following suit.

Before joining them, Twilight hugged her brother one last time, and said, "I'll see you on the other side, BBBFF." She then entered the TARDIS herself, and the strange blue box vanished from the War Room.

Changelingville

The TARDIS

A deep, dark dread permeated the TARDIS console room as the group made the return journey to Ponyville. Fear of what they might find gripped Twilight’s lungs like a vice, making speech difficult. It was clear from the unspoken silence that she wasn’t the only one feeling this way. Uneasy looks ran across the faces of the others, and she could only wonder what must be sitting on her own.

"We're close enough to Ponyville for a visual,” announced the Doctor, his shaking voice tearing the silence, “but I'm warning you, it's not pretty."

"Show us anyway," Twilight commanded.

She wasn’t fooling herself, they all knew to expect the worst, but nothing could prepare the group for the heartbreaking sight before them: Virtually every building had been shelled out in an attempt to deprive the enemy of cover, twisted husks of shattered gunships wantonly scattered across the ground beneath the sky that had been denied them, and ever prevalent throughout the town all manner of litter burned, yesterday’s garbage intermingling with last century’s antiques. Bodies, pony and changeling alike, lay rotting where they had fallen. Clearly, the enemy cared not to honour those who had lost. From Canterlot to Ponyville the destruction had been great, and the losses many. Twilight had to wonder, would they too end up like this, lying dead in a ditch with only the flies to remember them? Was this the fate of all who opposed the changeling horde?

"No…" came a soft voice to Twilight’s left. Derpy, the ever bubbly mare, looked as if she would never giggle again. Fluttershy herself seemed on the verge of tears as she took in the careless destruction of the carefully cultivated gardens. The Doctor, his jaw clenched as he gazed solemnly on the discarded dead. No, it would not end like this. Not her friends, not her family, not her. Not like this.

"Chrysalis will pay for this," Twilight growled, earning a glance from The Doctor. She was turning to glare back when she noticed something at the edge of the scan. Something… peculiar. "What is that? Doctor, move the view 30 degrees to the left," She instructed. The Doctor obliged, revealing an enormous twisted… something... The arcane eyepatch was making things a bit difficult, some colours were muted while others jumped into sharp relief and it reminded her of the time that she had stared at the sun for too long, but she thought she could make out dark thorny spines intertwining with slick green membranes. Regardless of how bad her vision might be, this was definitely not on par with standard Ponyville building code. “Looks like some sort of tower, perhaps it’s their base of operations?”

"Considering the damage to Town Hall, I doubt Chrysalis would have just set up shop there," The Doctor chimed in, “Ah, fantastic, we’re here”. There was an unnerving screech as the TARDIS engines ground to a shuddering halt. They had materialized.

"Where is ‘here’?" Fluttershy whispered, wiping her tears.

"Just outside Town Hall, or at least what's left of it," The Doctor explained. "It's as good a place as any to start our search."

"Won't we be surrounded by Changelings?" Derpy asked, coming up to the scanner.

"We shouldn’t have too much trouble,” Twilight shook her head, keeping her eyes on the TARDIS's scanner, “This spot looks pretty quiet. If we're lucky, some of the equipment in the War Room will still be functioning." Maybe we could get some answers… She swept around, brushing past them, "Well, we're on a tight schedule; let's get moving."

Ponyville, Town Square

She led the group out, and as they set hoof in the town square, one of the first things Derpy noticed was a smashed pair of violet sunglasses next to a pile of rubble. They had seen many rough parties, but it seemed that their viewing days were over. It was easy to guess what was under the rubble. "Vinyl Scratch. She was a DJ before the war." Derpy noted quietly, picking up the glasses, and placing them in a more respectful position on the makeshift cairn.

“Oh, THE Vinyl Scratch? The slayer of a million songs and the wubber of uncounted dubs?” The Doctor asked, "Such a pity, I’d always wanted to ask how exactly she came about that fantastic sound system of hers. Do you think her Bass Cannon would be salvageable?" He cast his eyes about the rubble hopefully.

"Probably not.” Twilight said, shaking her head, “Just before Town Hall was hit, she told me that the Changelings had sabotaged it. Odds are it's just scrap now." She then led the group into the torn and brown pavilion. Grown wild through neglect, there was really only one thing that stood out. Twilight trotted up to a conspicuously green and healthy shrub and with a brief exercise of mental muscle she yanked down on one of the branches. With an audible click the plastic shrub swung up and around to reveal a service hatch. "This will let out just outside the War Room." Opening the concealed hatch, they descended into the darkness.

War Room

Entering the war room, they found it in a state of disarray not unlike what they had seen outside. However, the smashed consoles and scorch marks on the walls indicated that this had happened all at once, a sudden storming of the fortress rather than simple decay and neglet. Broken glass and torn wires littered the floor, hazards seeking to add more to their dried pool of blood and ichor. A middle-aged mare lay sprawled on the ground, it seemed she had been abandoned, like all the others.

"Have they no respect for the dead?" Derpy asked huskily, throat swelling at the casual indifference with which the corpses had been treated. Fluttershy found a slightly shredded flag, and nervously laid it over the body.

"We'll give her a proper burial, don't worry,” Twilight reassured her, “But we need to look after the living first.”

She cast her eye around the crumbling command centre, the testament to Ponyville’s failures. Her failures. There didn't look to be anything worth salvaging.

"Twilight, I think I've found a working console." The Doctor called out from behind a jumble of wires.

"What have we got?" Twilight called back hopefully, trotting over and examining the screen. It was cracked and dusty, but it looked like the spell matricies and casting-processing-unit were still running. “Are those…?”

"Sensors, yes, and it looks like one of our shield generators is still running, aaaaatttt… Sweet Apple Acres!” the Doctor announced in a hopeful tone.

"That must be where everypony else is holed up, the generator wouldn’t run without somepony to keep it going!” Twilight surmised.

“Looks like you may be right, Twilight,” the Doctor nodded.

“Of course she’s right Doctor,” chimed Derpy, fluttering over the twisted mess of the floor, “The farm is totally the best hideout. After all, you know what they say: ‘an apple a day keeps the changelings away!’”

Twilight rolled her eye. “Come on you lot,” she called over her shoulder as she made her way out of the room, “Sweet Apple Arces is a good trot away and I’d rather we not get caught out in the open.”

“Umm, excuse me, but ummm,” Fluttershy whispered as the others filed out of the room, “Isn’t it ‘an apple a day keeps the doctor away’?”

“Silly Fluttershy,” giggled the cross-eyed mare, poking the shy one in the side, “All the apples in the world couldn't keep The Doctor away.” She looked off thoughtfully as she trailed out of the room. “Now a pear on the other hoof…”

Ponyville, Outskirts

Outside and along the open road again, the group had made it roughly three quarters of the way to Sweet Apple Acres when a crashed gunship caught Twilight's attention. Wrecks weren’t too uncommon, but something about this one was very familiar. She inspected the serial number on the side. A chill ran down her spine. Ah, so that was it.

"I know this gunship, it’s the Big Apple,” Twilight whispered, “It was crewed by Applejack, Pinkie Pie, Big Macintosh, and Caramel. I’m… I’m afraid to look inside…" Just one more failure… Exchanging a silent nod, the other two mares gave Twilight a hug and gently pushed past her, combing the wreck for their friends. The Doctor began fiddling with the electronics.

"T-Twilight? There's something you need to see in the cockpit..." Fluttershy called out. Steeling herself for the worst, Twilight hesitantly trotted over to see what had Fluttershy spooked. A grizly scene met her eye: a severed hoof lay pinned to the controls, pierced by a jagged piece of shrapnel the size of her head. Its orange coat was stained dark red and the surrounding seat was covered in dried blood. The owner, however, was nowhere to be found.

"A-Applejack..." Fluttershy squeaked, before Twilight cut in, "Let's not jump to conclusions. It looks like a clean cut, and there are no bodies, or other signs of a struggle here."

There a dull roar as the onboard generator sputtered back to life, followed by a sharp squeal as the intercom activated.

“…~om~omi-mi-mi-mised! Re…at! To…all has been compr….ed!” A stuttering country twang boomed out over the speakers, “Re-re-retreat to the seco-con-conndary base, and keep-ep-ep-ep ra-a-a-adio silence.”

“Gah!” exclaimed Twilight, “Applejack? Applejack! Where are you?” She twisted around, but only found Fluttershy and Derpy doing the same.

“Oooh! Ah! Sorry about that!” the Doctor poked his head into the cockpit, “I think I managed to find the flight records for when the ship crashed, maybe it can give us a clue as to what happened. Just give me a moment to reconfigure and… voila!”

Twilight listened carefully as the broadcast restarted, trying her best to sort out the mess.

~Seven Months Earlier~

A cacophony of noise burst over the speakers. Strained engines intermingling the sound of gunfire and screeching insects. One voice cut across it all. Female, country twang. That has to be Applejack.

"Town Hall has been compromised!” the country twang rang out, ”Repeat! Town Hall has been compromised! Retreat to the secondary base, and keep radio silence," The radio chirped as it ceased broadcasting.

“Al’righ Sugarcubes, them Changelings have won this battle, but we’ll see that Ponyville don’t go down without a fight! What do ya’ll say?”

"Applejack! Look out!" A high pitch warning rang clearly. That’d be Pinkie Pie.

A chittering screech followed by a tearing sound. Standard changeling attack spell, powerful, but avoidable.

A loud, screaming boom. Engine. Most likely port considering the damage we saw on the way in.

WooOoOOoosshhhh SceEeEeeee. Unbalanced flight. Fall.

"All hooves, brace for impact! This is going to get ugly!"

WHAM! Primary Impact.

RATTLE… WHAM! Bounce, turn, secondary impact.

KREEEEEEEEEEEEEEeeeeeeeeehhhhhh….Sliding and distortion of frame.

Huheh huh huheh huheh… Heavy breathing. Four patterns. No, three? No, definitely four.

"Is everypony alright?" Concern. Tenor. Male. Kind of whiny. Must be Caramel.

"Eeyup." Bass. Male. Stallion of few words. Big Mac.

"I'm okie-doki-loki, poki!." High pitch. Soul-gratingly cheerful. Pinkie Pie.

“EEEYYYAAAAAAAHHHH!!” Oh Applejack, what happened to you?

“On the other hoof, maybe no pokey. Wow, you got that stuck in there really good Applejack! This reminds me of the time when it was winter and I was mare-dared by my sisters to lick one of the metal rock shovels and I did it easy I mean what’s so hard about that but then my tongue got stuck and my sisters laughed at me even though I was totally daringly mare enough for that mare-dare and then I said…”

“EEEEYYYYYAAHH! MAKE IT STOP MAKE IT STOP!” No kidding, it’s like the last roundup all over again… Should have just given Pinkie a megaphone and sent her to the hive by herself.

"Ah'm going to try to pry that piece out." Big Macintosh.

"GYAH! NO, STOP, STOP! It's no good, Big Bro! It’s too jagged and too deep! Ah don’t think Ah’m going anywhere. You gotta go without me.” What! No! Don’t stay behind!

“Ah’m not leavin you, sis. Ah ain’t gonna leave you to the mercy of them critters. No way, no how.” Celestia bless you, Big Mac. Talk some sense into her.

“Y’all ain’t stayin here, Ah won’t have you dyin’ on my account! Ah can’t have your blood on my hooves.”

“And Ah can’t have yours on mine, sis”

“...And that’s I met Gummy! Whew, I haven’t told that one in a long, long time. It’s a zinger! Hey Applejack, why are you still hanging around on the floor? Don’t you know that if there’s something you can’t bring with you, you should leave it behind?” Pinkie…

“See Bro, even Pinkie understands.”

“The answer’s no, and that’s final. Ahm not leaving you behind”

“Silly billy, whoever said anything about leaving Applejack behind? Just use this!” Use what?

“Ms. Pie, what are you… where did that even come from?” What is it!?

“Oh, this is Mr. Cleavy! My mother always told me that a mare’s always gotta be prepared, no matter the scare, so that I can be fair and show the scary scare a good ‘beware’! I sometimes use it to cut cakes, but don’t tell my mom, she’ll just lecture me about proper care of an ethyl leprechan, and I don’t even know where to find one of ‘my little alchoholics’!”

“Ah… Ah uh… Ah don’t even know where to start with that one.”

bzzzzzzzzzzzzzzzzz Uh oh, sounds like the changelings are coming back.

"Ngh.. The way ah see it, big brother, you've got two choices: amputate, or leave me here to die."
bzzzzzzzzzzzzzzzzz

"No! Ah won't cut off mah own sister's hoof!"

bzzzzzzzzzzzzzzzzz

"It's better than the alternative."

Bzzzzzzzzzzzzzzzzz Uh, they’re getting closer guys

“But…”

BZZZZZZZZZZZZ Guys?

"Forgive me." The deep bass rumbled painfully.

BZZZZZZZZZZZZ!!!

There was a sharp intake of breath and…

KTCHTZZZZZZZ…

Present

Twilight shook her head to clear it; that had been… intense. She could still hear the buzzing of changeling wings as they had closed in on the crashed ship. "Alright, we know Applejack's probably still alive, or at the very least, this isn't what killed her,” she pointed out, taking a quick look around.

Fluttershy was staring wide eyed at the speaker, shaking slightly. The Doctor was looking thoughtfully at his own right hoof. Derpy, well, it was hard to tell which way Derpy was looking, but it certainly seemed she hadn’t really enjoyed the audio drama that had just unfolded. She stomped her hoof on the warped floor, earning a resounding clang, “We've wasted enough time here; we need to get moving again." She flipped the intercom off. The static ceased. The buzzing did not. It grew louder. Uh oh. “Everypony move!” She screamed, bolting quickly out of the ruined war machine.

"Too late! The onboard generators bust have attracted their attention" The Doctor cried, as a squad of Changelings swooped in on them.

Twilight opened fire, slinging potent magic missiles with her horn. Fluttershy and Derpy took to the skies to engage them hoof to hoof. Chiropractic techniques turned deadly as Fluttershy executed a perfect aerial suplex, smashing a shapeshifter into the ground. Derpy took a less direct approach, goading the demons into chasing her in and around the unstable hulk, her erratic flight path compromising the remaining integrity and bringing it down on her pursuers. The Doctor used his sonic screwdriver to sow confusion among the shifters’ ranks, the high frequency waves scrambling their concentration and destroying their disguises.

Even so, they were outnumbered three to one, and with one group already here, there were sure to be more on the way. Suddenly one of the flying demons, making a dive for Twilight’s unprotected back, screeched in surprised as a pair of emerald mana blasts tore the wings from it’s own back. Landing stunned, it had only a moment to look up before a pair of perfectly harmonized followup blasts flash-fried it. After that, the Battle of the Big Apple quickly fell to the ponies’ favour, and the mop-up of the Changeling scouts was relatively uneventful. Once the dust had cleared, Twilight quickly worked to identify their mysterious rescuers. Hmmm, two ponies. Same stature. Same red hair. Same green aura. Same RIDICULOUS salesman outfits. Could it be…

"Flim and Flam?" she asked, incredulously. What are they doing here? Why did they help us?

"She's been wondering when you'd make your way here," Flim remarked.

"Who? Chrysalis?" Fluttershy asked.

"Not exactly. Come with us, and we'll explain everything," Flam answered. "Oh, and Commander, sorry about your eye."

Sweet Apple Acres

The barn was a glorious sight to see. Painted in bright, friendly colours, it served as a stark contrast to the dilapidated wasteland that Ponyville had become. The group was asked to wait at the entrance to the barn while the Flim Flam brothers sent for their boss. They could hear her hoofsteps, and Twilight noted that one sounded distinctly… heavy. Her look of concern quickly turned to elation as this mysterious mare turned out to be Applejack, flanked by Rainbow Dash and Pinkie Pie. The hoof she had lost had been replaced with an artificial one, evidently cobbled together out of what was available, which apparently meant a spatula, a tuning fork, several lengths of chickenwire and what appeared to be the family toaster. Twilight thought it looked pretty ridiculous, but Applejack wore it like it was her own flesh and bone. Twilight and Fluttershy rushed into the room, and all tension was gone as the five friends joined in a group hug. Twilight noticed Pinkie Pie's mane returning to its poofy self, though she could have sworn she saw a glint of steel before it was lost in the tangled mass. The Doctor and Derpy, not quite comfortable to be part of the inner circle, instead opted to sample from the celebratory cider table that had been set up.

"I can't believe you're still alive!" Twilight exclaimed.

"The feeling's mutual, Twilight," Applejack replied.

"Wait, w-where are Spike and Rarity?" Fluttershy asked. The mood darkened faster than like a lonely library in a Vashda Nerada spore swarm.

"Anypony who was still alive in Town Hall would have been brought to the Hive.” Rainbow Dash sighed, as the hug broke up. “I think it’s that huge weird tree that they’ve got growing. ", breaking away from the group hug.

"That complicates things." Twilight commented.

"What do mean, Twilight?" Pinkie Pie, hopping around like she was some sort of orbiting moon.

"We brought the Elements of Harmony with us, so we could take out the barrier from the inside, but I guess now we'll have to storm the Hive first." Twilight explained.

"We might be able to help with that." Flim piped in.

"That's the other thing I don't understand,” she pushed on, ignoring him, “You're working with the Flim Flam brothers. Do you have any idea what they did?" Twilight inquired candidly, keeping her voice dangerously calm. They killed Mayor Mare, shot me in the eye, and sold Ponyville out!

"Actually, yes, Twilight, Ah do: They killed Mayor Mare, shot you in the eye, and sold Ponyville out."

"And you trust them!? For all we know, they're still working with the Changelings!" Twilight pointed out.

"We are working with the Changelings, against Queen Chrysalis." Flam answered.

"Have you lost your mind!?" Twilight demanded. This is unbelievable!

"They reached out to us telepathically. The average changeling has no desire to wage war on us, but due to the control Chrysalis exerts over the hive mind, they have no choice." Flim clarified.

"You expect us to believe that?" Twilight questioned them.

"Actually, Twilight, it makes sense.” The Doctor interjected, “Remember the psychic interference I sensed around Larva?" Well…

"But... don’t they object to you killing them?" Fluttershy asked, turning great, confused eyes on the two twins.

"An act of mercy, compared to living under Chrysalis's control." Flim answered flippantly, "By Changeling standards, she's an insane monster." That sounds surprisingly close to my standards too… Ngh... Curse these ponies, they drive me to drink.

"Anyway, Twilight, Ah had a plan to take down the hive, but we just don’t have the numbers to pull it off." Applejack added.

“Now THAT we do have,” Twilight smirked, dragging a fresh, foaming tankard over, "Don't worry about that. The cavalry's on the other side of the barrier, just waiting for us to take it down." With a wary glance at Flim and Flam she threw her head back and drained the tankard, then slammed it down and wiped the foam from her lips. "Now, let's hear this plan of yours.”

Author's Note

Special thanks to Luminous Lead for expanding this chapter.

Showdown

Ponyville, Outskirts

All was quiet over what was once Ponyville. The Changeling patrols around the ruined town had died down, concentrating instead on fortifying the Hive, aware that ponies had breached the barrier, and were preparing to attack. In a secluded spot outside of Sweet Apple Acres, Twilight and Applejack waited for their plan to commence, keeping a close eye on the shield over the farm.

"Sweet Apple Acres is cleared out, and the demolition teams are in position, Twilight." Rainbow Dash sent out over the radio.

"Good. Don't fire until you get the signal." Twilight sent back.

"Are you sure about this, Twilight?" Applejack asked, lowering her binoculars for a moment.

"Without Lt. Heartstrings powering the shield generator, it'll drop in a matter of moments. Thinking they've won, the Changelings will flock to it like moths to a flame, only to be hit with the biggest bug zapper in Equestrian history." Twilight explained.

"That's what ah'm afraid of." Applejack remarked.

As if on cue, the shield surrounding Sweet Apple Acres vanished, leaving the farm defenceless. As Twilight predicted, swarms of Changelings flew out from the Hive to secure the farm.

The Hive, Feeding Chamber

"My Queen, we have Sweet Apple Acres surrounded." One of the Changelings sent out through the hive mind.

"Excellent. Do a thorough search, and bring every last pony here." Chrysalis instructed. Turning to a restrained Rarity, she asked "What do your friends think they're doing? What do they hope to accomplish? No matter. Their struggle for freedom is over. You're all mine now."

Rarity tried to protest, but anything she tried to say was muffled by a gag.

"Struggle to your heart's content. You've already lost." Chrysalis said to her. Then, her minions reached out to her again through the hive mind.

"The farm is now secure!" They explained.

"Good work. And the ponies? Have they been rounded up?" Chrysalis asked.

"We haven't seen a single pony here. It's nothing but explosives and timers." The changeling explained.

Suddenly Chrysalis realized what they were up to. "What? Get out! Get out of there!" She screamed, both vocally and in the hive mind.

Ponyville, Outskirts

It was too late. Within seconds, the first set of charges had gone off, lighting the walls of the barn on fire. Soon after, the second set went off, completely ripping the barn apart, and incinerating any changelings inside. Next came a set strewn across the farm, clearing out any that might have been outside. In just over a minute, Sweet Apple Acres had become nothing more than a burning crater, taking a good chunk of the Changelings' forces with it..

Shocked and horrified by her own actions, Applejack asked, "By Celestia, Twilight. What have ah done?"

"What you've always done. You saw the ugly truth, and you faced it head on. I know how hard it must have been to wilfully destroy your own home, but you knew the chance it gave us." Twilight said, trying to reassure her. "We need to rejoin the others."

Outside The Hive

Rainbow Dash examined the destruction of Sweet Apple Acres through her binoculars, commenting, "That's the signal." Putting down the binoculars, she called out, "Fire!" and a volley of missiles slammed into the Hive's outer wall. While they hadn't initially built much in the way of hoof-held weapons, they had managed to cobble together several rocket launchers using parts salvaged from the downed gunships. Stability aside, the makeshift bazookas proved powerful enough to blow a sizable hole in the Hive's wall.

The Hive, Feeding Chamber

Seething in anger at the massacre brought forth by Applejack and Twilight, Chrysalis tore out Rarity's gag and said, "Evidently, your friends are more resourceful than I anticipated. You have insisted on taking the place of our other feeding victims for months now, so believe me when I say, I'm going to enjoy this."

With the slightest hint of desperation and weariness in her tone, Rarity responded with, "Feed on me all you want, you monster! They're coming for you!"

With a smug grin, Chrysalis said, "Oh, my little pony, you misunderstand me. I'm not going to feed on you. I'm going to make you watch."

The door to the chamber opened, and two Changeling guards pushed Spike in. In response, Chrysalis took Rarity's form, and said to her, "As I feed on him."

Outside the Hive

Twilight and Applejack arrived at the scene to find Changelings spilling out of the hole created by the demolition teams, and ponies engaging them by any means available. Along with ponies fighting the Changelings hoof to hoof and via magic missiles, Twilight could also see ponies from the demolition teams firing their unused rockets into the fray, and she could swear she saw Pinkie Pie swinging a cleaver around.

"Pinkie!" Twilight called out. "Forget them! We have to get inside." She then charged into the fight, firing a few shots at the nearby Changelings. Just as she made it, a stray rocket impacted nearby, knocking her to the ground. A changeling who survived the blast attempted to pounce her, only to be hit by an uppercut from what looked like a toaster attached to a pony's foreleg. Twilight got back on her hooves, and turned to face the orange mare who had saved her.

"Thanks, Applejack." Twilight said to her. Until now, she hadn't realized how useful Applejack's artificial hoof could be in a fight.

"Don't mention it, Twilight. Come on. Fluttershy and the Flim Flam brothers are already inside the Hive. Ah'm sure Derpy can handle things out here." Applejack instructed.

The Hive, Entrance

Just as Twilight and Applejack made it inside, Twilight asked Flim, "Remind me again what sort of resistance we can expect now that we're inside."

"Minimal, Commander. The majority of their forces were either take out in your little trap, or they're engaged outside." Flim explained.

"This place gives me the creeps." Rainbow Dash commented, and while she could speak for herself, Twilight suspected everypony in the group shared that sentiment. The walls and ceiling were all black, with just the slightest hint of green to make them unnerving, and they were twisted, yet rigid, cold, yet organic. She didn't want to spend any more time in here than she had to.

"Lead the way to the detention block." Twilight then instructed the brothers.

"Right away, Commander. There's just one thing, though. The Changelings don't call it a prison. They call it storage." Flam pointed out.

The Hive, Storage

'Prison' was certainly not the right way to describe this chamber, but Twilight had nothing she could truly compare it to. The room spanned the entirety of the level, and across it, ponies hung from the ceiling in individual pods. Like the rest of the Changelings' designs, the pods appeared to have been grown organically. Before she could say anything, Fluttershy took a look at the closest pod, and said, "It's Vinyl Scratch. But how? She's dead. We saw her body and everything."

"No, we didn't, Fluttershy. We saw her glasses next to a pile of rubble, and we assumed her body was under it." Twilight corrected her. Then, she said to the group, "Alright, everypony. Let's fan out, and start freeing these prisoners. The sooner they're freed, the sooner we can take out the barrier."

Even with their combined efforts, it still took a considerable about of time to free all of the prisoners. Once they were done, Twilight gathered her friends back at the entrance to the room, and asked, "Well, any sign of Rarity or Spike in there?"

While they all answered with some form of "No.", Rainbow Dash added, "I did see a couple of empty pods, though."

"The pods are grown as needed, and destroyed once they're no longer needed." Flim explained. "There's only one reason for them to be empty: feeding."

Suddenly, Twilight realized the consequences of taking the time to free all the prisoners. Both Rarity and Spike could have died from overfeeding by now.

"Then where would they be?" Fluttershy asked.

"The feeding chamber. This way." Flam said, taking the lead again.

The Hive, Feeding Chamber

What the group saw as they arrived in the feeding chamber was horrific in its own right: Rarity was tied to a post in the middle of the room, and Spike was crumpled on the floor, barely conscious.

"No." Twilight said and tears started to flow from her eye as she ran to Spike.

"Twilight...I knew you'd come back for me." Spike tried to say, but Twilight could tell he was very weak, most likely from being fed upon.

"Rarity, what happened?" Twilight asked.

"Chrysalis brought me in, as if she was preparing to feed on me, but then she made me watch her feed on Spike instead." Rarity explained. In contrast to Spike, she appeared to be unharmed, at least physically. "She knew feeding on him would hurt both of us more."

Twilight cradled Spike in her forelegs, as Pinkie Pie and Fluttershy broke Rarity free of her restraints.

"Just hang on, son. We'll get you help." Twilight said to him, but all signs told her he wouldn't make it.

"Too late, mom. I'm just happy I could see you, one last time." Spike said to her with a smile on his face. Unfortunately, it was the last thing he ever said.

"Me too. Goodbye." Twilight said back to him. Is how my parents felt, when they thought I had died? She thought to herself, giving Spike's body a kiss on the forehead, and then closing his eyes out of respect. Spike was the closest thing she had to a son, and now he was gone.

After a moment's pause, Applejack said, "It's time.", and passed Rarity's Element to her.

"For Spike." Twilight said as her Element started to glow, and the others repeated it after her. The Elements of Harmony sent a flare out, though the walls of the feeding chamber, and out to the top of the Barrier.

Outside the Barrier

Shining Armour watched intently as the Barrier surrounding Ponyville shattered. For a moment, he was taken aback by the state of the town, but he called out, "Attack!" and the gunships flew forth, with hoof soldiers following right behind them.

The Hive, Feeding Chamber

With the barrier down, the group could hear the sound of heavy rain from outside.

"We should get out of here. My brother's forces will be here in moments." Twilight instructed. "I'm surprised we didn't run into Chrysalis at all. Rarity, where did she go after she fed on Spike?"

"She went upstairs to an observation level. It would be easier for her to coordinate the Changelings below from up there. Now that the barrier's down..." Rarity answered, but she stopped dead in her tracks at the sight of the Changeling Queen.

"Is it? It is. Commander Twilight Sparkle, returned to reap what she's sown. Gaze upon the fruits of your failure!" Chrysalis said as she eyed up Twilight.

"Chrysalis. It ends now." Twilight responded, her tone suggesting she was holding back intense anger and rage.

"Of that, I have no doubt." Chrysalis released a massive beam of energy from her horn, and while they were all able to dodge it, Twilight was certain it would have killed her. As Chrysalis charged her horn for second blast, Twilight took the opportunity to leap out of the way and tackle her, the resulting force pushing both of them through the doorway behind Chrysalis.

The TARDIS

Having correctly guessed at its use as a makeshift command centre, Shining Armour stepped into the TARDIS to find the Doctor, Derpy, and several other ponies overseeing the battle outside.

"Captain, I'm glad you're here." Derpy called out from the console.

"Where's Twilight? We've got gunships position, ready to open fire on that Changeling structure." Shining Armour asked.

"Tell them to hold their fire; your sister and her team are inside!" The Doctor shouted back at him. "One of the Element Bearers was being held prisoner, so they had to break her out before they could take out the barrier. In addition, there appear to be several prisoners still inside. Our side of the entrance Twilight's team used is still too hot to use, and none of our radio transmissions seem to get through."

"What about the damage to Sweet Apple Acres? That looks fresh." Shining pointed out. The pattern by which the farm was destroyed didn't match up with how the Changelings fought.

"Wilfully destroyed, in order to thin the Changeling numbers." Derpy explained.

"Let's hope it was worth it." Shining Armour commented.

The Hive, Stairwell

Twilight had no delusions about her abilities. No matter how she looked at it, Chrysalis outmatched her in terms of magical ability. The only way to hold her own in this fight was to keep her wits about her, and hold off on resorting to brute force. So far, it seemed to be working, although one of them seemed to always be pushing the other further and further up the stairs.

"That little trap at Sweet Apple Acres had you written all over it." Chrysalis said to her, taking swing at her with a forehoof.

"I may laid the same trap twice, but you fell for it both times." Twilight retorted dodging it yet again.

"Do you think that justifies the blood on your hooves?" Chrysalis asked.

"Don't play innocent. Where killers are concerned, I'm nothing compared to you." Twilight responded, taking the opportunity to charge, and drive her horn into Chrysalis's gut. Chrysalis reeled back from the pain, and then kicked Twilight the rest of the way up the stairs.

The Hive, Top Level

Twilight looked around for a moment, getting back on her hooves. Apart the roof supports, this level appeared to be completely open to the outside, and it was a long way down. She got herself away from the stairs, and opened fire at the first sign of Chrysalis. The shot missed, and Chrysalis fired an explosive blast at Twilight. Twilight was able to avoid the shot, but the force of the explosion propelled her to the edge of the platform. Before she could get up, Chrysalis landed on top of her, and charged up her horn to fire again.

"I should have killed you at the first chance I had. Time to correct that mistake." Chrysalis said, but before she could fire, Twilight slipped out of the way, punched her in the horn wound she had created earlier, and then slammed her hoof into the back of Chrysalis's neck, bringing the Changeling Queen to the floor. Twilight then pressed her hoof down on Chrysalis's neck, effectively strangling her.

"You took away my life, destroyed my home, caused nothing but pain and suffering to everypony I held dear." Twilight said, pushing down harder.

"You ... wouldn't." Chrysalis said, struggling to breathe. Twilight raised her hoof from Chrysalis's neck, and then brought it down on the Changeling Queen's horn, shattering it. She heard hoofsteps coming from the stairs, and turned to see her friends looking back at her. I'm better than this. She thought.

Twilight turned back to Chrysalis and said, "You'll live. Surprised? Don't be. You're not worth killing. Equestria will always endure. Remember this defeat, this humiliation. Remember you can never win."

Chrysalis replied with a simple, "You should have killed me when you had the chance." And she slipped off the edge of the balcony, but when Twilight peered down after her, she was nowhere to be seen. Twilight also noticed that the fighting had mostly subsided. She turned back to her her friends, and called out, "Let's go. I've had enough of this place."

Outside the Hive

Leaving the Hive, Twilight saw her brother supervising the cleanup, and embraced him in a big hug.

"Twily! You made it out alive!" Shining Armour exclaimed at his sister's embrace, before taking a closer look at her. "Is that Changeling blood on your horn?" He asked.

"I'd rather not talk about it. What happened down here?" Twilight asked, breaking away from the hug at the mention of the blood on her horn.

"Just before Chrysalis fell, most of the Changelings surrendered, and the rest flew off." Shining Armour explained.

"And Chrysalis? Did you find her body?" Twilight inquired, though she didn't expect much of an answer.

"Twily, we didn't even hear her land." Shining Armour answered. "She must have teleported in mid-fall. Look at the bright side, Ponyville is back in our hooves!"

Twilight smiled at that, but then she took a deep breath, and said, "Shiny, Spike..." It was all she could bring herself to say, and it was all her brother needed to hear. Shining hugged Twilight again, and both started to cry. He knew Twilight had considered Spike her son, and that basically made Spike his nephew.

"I'm so sorry, Twily. I know how much he meant to you." Shining said, trying to comfort his sister. Even if Ponyville could be rebuilt, it would never be the same as it was.

Author's Note

Please note that there will be an epilogue after this.

Epilogue

[youtube=0Snbjr-sRFg]

Canterlot, Prison
Three Weeks Later

Princess Luna approached Larva's cell, flanked by Twilight and the Doctor.

"Ah, Princess Luna. It's so good of you to drop by. Where's your lovely daughter and her oh-so trigger happy husband this time?" Larva asked.

"Helping with the repairs to Ponyville. We didn't come here just to chat. We want information, starting with where Chrysalis fled to." Luna inquired.

"Very well. She fled to the deepest part of the Everfree Forest, to recuperate from her losses in Ponyville." Larva explained.

"You're certainly more forthcoming than last time." Twilight commented. Based on what she had seen of the Changeling Prince before, this was most confusing to her.

"My mind was not my own. It is now." Larva elaborated. Instinctively, Luna turned to face the Doctor, as if silently asking him a question.

"He's telling the truth. The psychic interference I sensed before is gone." The Doctor answered, having little difficulty interpreting the gesture.

"How?" Twilight asked the Changeling, still unsure of what effect this development would have on the war.

"When you destroyed Chrysalis's horn, you did not strip her of all her magic, but you did weaken her enough for me, and other changelings like me, to regain our free will." Larva explained to them.

"And that benefits both our races, does it not?" Luna surmised.

"On the contrary. Without a dominant monarch, the Changelings of my level will turn on each other, vying for total control of the Hive Mind, each one commanding an equal portion of Chrysalis's forces. Once one emerges from the civil war victorious, you'll be back where you started." Larva elaborated. "Chrysalis may even regain control. Release me, and if I become King of the Changelings, I promise you, all of my race's hostile action against yours will cease."

"Why do you want to help us, Larva?" Twilight inquired.

"Have you ever thought about the problem with a race that feeds on love declaring war on a race that's so full of it? By attacking you, Chrysalis was effectively poisoning our food supply. Look at yourself, Commander. Your hatred for Chrysalis is so intense, that no disguise could get past it." Larva answered. "On the other hoof, an alliance between ponies and changelings will provide use with all the love we need, with no harm done to the ponies involved."

Luna thought for a moment, and then cast a spell to unlock and open Larva's cell. "I have one additional condition for form this alliance: all pony prisoners in your hive must be released, starting with Princess Celestia."

Stepping out of the cell, Larva said, "That is acceptable, but we do not have Celestia."

"You said the Changelings were feasting on her!" Twilight rebuked.

"And in doing so, they brought forth a monster they could not control." Larva explained, angering Twilight further.

"Celestia is not a monster!" She shouted at him.

"How well did you know her? There's nothing feeding brings forth that the pony isn't already capable of." Larva asked, glaring back at Twilight.

Seeing the tension growing between Twilight and Larva, the Doctor cut in, saying, "If you don't mind, Prince, I'd like to discuss a few things in private with my colleagues."

The Changeling Prince nodded, and the three ponies stepped out of the cell block. Once of out earshot of Larva, the Doctor asked, "Do you really think it's wise to be antagonizing him like that, Twilight?"

"Do you really think it's wise to be allying ourselves with him? He spent three months sabotaging our efforts!" Twilight answered.

"He wasn't acting of his own accord; we can't judge him now based on that." Luna pointed out. "Besides, there are other threats to Equestria, and we need all the allies we can get."

"Such as?" Twilight asked. While she had seen the threats posed by both Nightmare Moon and Discord before this, she hadn't seen any serious threats, beyond the Changelings, of course, that took more than the Elements of Harmony to stop.

"I'm sure you understand why the Changelings left the city of Whitetrot alone." Luna started.

"It's one of the northernmost cities in Equestria, and Changelings can't survive in that cold a climate." Twilight explained.

"Not all of our enemies have such a weakness. A thousand years ago, there was another city that far north, known as the Crystal Empire. Its king, a unicorn named Sombra, had gone mad with power and enslaved the population. Celestia and I combined our power, and were able to banish Sombra into the shadows, but he managed to take the city with him. A month into the war with the Changelings, it resurfaced, but I felt we couldn't devote the necessary resources to securing it, so Sombra reclaimed it with little effort." Luna elaborated.

"You think that if we have Changelings helping us in the more temperate parts of Equestria, we'll be able to retake the Empire sooner." Twilight surmised. "I still don't trust Prince Larva, but I do trust you, and it's your call, Princess."

Ponyville
Two Years Later

Today was a good day. Ponyville had been restored to its former glory, and in a matter of hours, the peace treaty between ponies and changelings would be signed. King Larva had been true to his word, and put a stop to all Changeling aggression after he killed Chrysalis and established himself as the dominant Changeling. As the Doctor predicted, Luna had her seat of power moved from Canterlot to Ponyville once the restoration efforts had gotten underway.

Twilight looked back on the last three years and everything she had seen and lost in that time. Spike, her Number One Assistant was gone, and it was likely she would never see Princess Celestia again. She knew it meant she could never complete her studies, or become the princess Celestia had intended her to be, but somehow she also knew that from here on out, everything was going to be just fine.