Doctor Whooves: World War Equestria

by Draconaquest

Rating: teen
Tags: Science Fiction, Crossover, Tragedy, Dark, Alternate Universe, Drama
Length: 9778

Chronicling the events of the Crystal War, after the Doctor arrives, becoming the chief tactician for the Equestrian Army.

Shortly after regenerating, the Doctor falls into a parallel universe, where Equestria is at war with the Crystal Empire. Falling into the military, the Doctor becomes the Head Tactician for Equestria, alongside Brigadier-General Rainbow Dash, and the Pie Sisters.
This story chronicles the events that happen in this timeline.
The story before this is not required to read before reading this, as it does not directly impact this story.
WARNING: Much creative license has been used.
Takes place in the Sombraverse seen in The Cutie Re-Mark.

Published 1970-01-01 00:00:00 UTC
Last updated 2016-05-08 23:13:59 UTC

Arc 1, Chapter 1: The Doctor and Dash

Despite being very active throughout the day, Cloudsdale was very quiet during the night. Most of the Pegasi were sleeping, so few noticed loud noises. They dreamt about the following days, or the sheer tranquility of Equestria, and how it would never end.

Rainbow Dash wasn't one of these ponies. She had difficulty sleeping. Every time she laid down she was always uncomfortable. She was constantly fidgeting, readjusting her wings, and trying to get comfortable. After going through the same thing every night, she frustratingly got up, and started moving around. Whether she got a midnight snack, or exercised, or simply wondered around the house, she never slept, unless she was dead tired.

So, once again, Rainbow groaned and sat up. "One good night's sleep!" She shouted to the air, "All I want is one good night's sleep!" She got out of bed and stretched her limbs. Wings, legs, neck, tail. The same order as every night. "I mean seriously! I need either a more comfortable bed, or a medicine which will help me sleep. That would be a great doctor, one who helps with sleep." She sighed, and looked at her wall. Yep, the crack was still there.

Rainbow knew that a crack in the wall wouldn't simply just go away, it needed to be repaired, but she still silently hoped it would disappear. "Maybe I should call a policeman. Yeah. that'll work." She looked to the ceiling. "I hereby summon a policeman, to fix my wall!"

She sighed, and walked over to her desk, and sat down in her chair. Blitz had bought her a diary to write it, but she never used it. She wasn't that type of girl.

Her brother still had to get it through his skull that she wasn't a stereotypical girl, who wanted to be an alicorn princess when she grew up. She got sick of that. Literally, she became ill. She wanted to be a Wonderbolt, one of Equestria's finest flyers. That was her dream. That is what she wanted to do. But, no one else supported it. Sure, Blitz had gotten her into flight school, but he would take any extra steps to help her.

It got old sometimes. Maybe it was just her, or maybe she just needed to give Blitz a push. It didn't matter. She would get there one day. For now, she just had to plow through.

Rainbow leaned back in her chair, and listened to the night. It was quiet, unbelievably quiet. Then she heard something new. A groaning, wheezing sound filled the night. The pitch got higher, and higher, and stopped with a loud crashing sound.

She stood up, and looked out the window. Sitting in her front yard on the clouds was as a blue box, about six feet tall. Written on the top in glowing letters was 'Police Public Call Box' and it was on all four sides.

"What the...?" Rainbow mumbled, and trotted out of her room. Maybe someone up in the sky had heard her. She grabbed a flashlight with her mouth, and left the house, into the courtyard. Walking on clouds was easy to the Pegasi, though other races of ponies couldn't. It's a detail Rainbow always found interesting.

Rainbow walked toward the box, and gazed at it, the flashlight illuminating it. Then, something unexpected happened. The doors on the front slammed outwards, causing Rainbow Dash to drop her flashlight in surprise. A grappling hook flew out of it, latching on to a nearby wheelbarrow. The rope tightened, and a hoof soon appeared, grabbing into the exit of the box. Another hoof appeared, and then a head.

It was a stallion's head, and he seemed slightly confused, as his mane was soaking wet and brushed back. He looked down at Dash, and said, with all sincerity, "Can I have an apple?"

Rainbow's face scrunched up. "I'm sorry?"

"It's all I can think about," the stallion said, "Apples. I love apples. Maybe I'm having a craving! That's new, never had cravings before." The stallion pulled himself up, and swung one leg over the edge of the box, before looking in it on awe. "Oh! Look at that!"

Now Rainbow could get a good look at him. He was wearing a white dress shirt, complete with a green tie, with brown pants. Though, his clothes were torn up, and sticking out and loose. Okay Rainbow, be nice. She thought to herself. "Uh... are you okay?"

The stallion swung his other leg over the edge, and was now facing Rainbow completely. "Just had a fall." He said, adjusting his sleeves, "All the way down there right to the library. Hell of a climb back up."

"You're soaking wet."

"I was in the swimming pool."

"Didn't you just say you were in the library?"

"So was the swimming pool."

Rainbow shook her head violently, and looked back at the colt. "Are you a policeman?"

"Why?" The stallion asked, and leaned forward slightly. "Did you call a policeman?"

"Did you come about the crack in my wall?" Rainbow asked, hopefully.

"What cra-a-ack!" The stallion clutched his chest in pain and fell off the box to his side.

"Whoa!" Rainbow gasped, "You okay?!"

"Oh, I'm fine!" He said, sitting up and waving his hoof. "It's okay, this is all perfectly norm-" He coughed, as golden energy left his mouth and floated into the air.

Rainbow looked in awe. "Wh-who are you?"

The stallion stuck his hooves out in front of him, as golden energy slightly seeped off them. "I don't know yet. I'm still cooking. Does it scare you?"

"What?" Rainbow asked, "No no, it just looks...weird."

"No no no, the crack in your wall, does it scare you?" The stallion asked, his eyes beaming.

"Uh..."

"Now come on, don't be shy, just answer the question."

"It-it does."

The stallion grinned, and jumped to his hooves. "Well then, no time to lose!" He grinned down at Rainbow. "I'm the Doctor. Do everything I tell you, don't ask stupid questions, and don't wander off." He turned and walked off...

...right into a pillar, causing him to topple over. Rainbow looked down at him. "You alright?"

"Early days. Steering's a bit off."

The Doctor looked around Rainbow's kitchen, as she trotted back over to him, holding something. "So, if you're a doctor, then why does your box say 'police?'"

The Doctor grabbed the item from Rainbow and took a bite out of it, before immediately spitting it out. "Oh, that's disgusting..." the Doctor coughed, "What is that?"

"An apple."

"Apples are rubbish, I hate apples."

"But you just said you loved them!"

"No no, I love yogurt! Yogurt's my favorite, give me yogurt!" Rainbow groaned, and went over to her refrigerator before returning with yogurt.

The Doctor seized it from her, popped it open, and poured it into his mouth, before spitting it out across the room. "I hate yogurt, it's the stuff with bits in it."

"But you just said that was your favorite!"

"New mouth!" The Doctor said, rubbing his mouth clean of yogurt, "New rules! It's like eating after cleaning your teeth, everything tastes WRONG!!!" He jolted into several positions, before returning back to normal.

"Geez, is something wrong with you?" Rainbow asked.

"Wrong with be?" The Doctor responded, "Why can't you give me some decent food? You have a stove, fry something."

Rainbow Dash proceeded to turn on the stove and cook more food. "Ah, there we go! Daisies!"

Once the fries were finished cooking, the Doctor popped one into his mouth, smiled a bit, and then started to smile a bit, before sticking his tongue out and flicking away the food. "Daisies, that's daisies? Are you trying to poison me?"

Rainbow raised an eyebrow, before returning to the stove. "Ah, you see? Beans."

But, once the Doctor took a spoonful, he ran over to the sink, and spit them out. "Beans are evil. Bad bad beans."

A few minutes later, Rainbow was scraping butter onto a slice of bread. "Bread and butter." The Doctor said, approvingly, "Now you're talking."

It only took a single bite. The Doctor ran to the door and threw the bread outside. "And stay out!"

Rainbow continued to look in her fridge. "Let me guess, you don't like carrots either?"

"Carrots?" the Doctor gawked, "Are you insane? Oh, wait! I know what I need!" He trotted up to the fridge. "I need, I need, I need....hay fingers... and custard." He pulled the items out of the fridge, and with a massive grin, closed it.

The two sat in silence as they ate their respectable food. Rainbow was enjoying ice dream and a cup of apple cider, whilst the Doctor, sure enough, was dipping hay fries, or as he called them hay fingers, into the bowl of vanilla custard.

Rainbow stared at his with a confused look. "Well, you're funny, I'll give you that."

"Am I?" The Doctor asked, "Good. Funny's good. So what's your name?"

"The name's Rainbow Dash." The pegasus replied proudly, putting a hoof on her chest.

"Oh, that's a brilliant name!" The Doctor replied, causing Rainbow Dash to blush, "Rainbow Dash... sounds like a name in a fairy tale." That line caused Rainbow to frown. "Are we in Cloudsdale, Rainbow?"

"We are," Dash replied, "I'm currently enrolled in flight school. It's... kinda boring. I'm already better than all the Pegasi there, and maybe even the teachers. There's nothing they can teach me that I don't already know."

The Doctor raised an eyebrow at her boasting. "So where are your mum and dad then? I thought we'd've woken them by now."

Dash sighed. "I don't have a mom and dad. Just a brother." She groaned with distaste.

The Doctor swallowed. "I don't even have a brother."

"Lucky you."

"I know." The Doctor grabbed another hay finger, "So your brother then, where's he?"

"He's out, spending some quality time with a mare he met last week." Rainbow snorted, "He thinks I don't know what he's up too."

"But he left you all alone?" The Doctor asked.

"What do you think I am, scared?" Rainbow challenged.

"Of course you're not," the Doctor scoffed, "You're not scared of anything! Box falls out of the sky, colt falls out of the box, colt eats hay custard, and look at you! Just sittin' there. Cause you know what I think?"

"What?" Rainbow asked.

"You're scared of a scary crack in your wall."

Arc 1, Chapter 2: The Crack in the Wall

The Doctor trotted toward the crack, Rainbow Dash at his tail. He look at it, and knew what it was. "You've had some cowboys in here. Well, not actual cowboys. Though that can happen." He looked at Rainbow, who was holding an apple.

"I never liked apples. Then my mom put faces on them." Rainbow said, handing the apple to the Doctor, who looked at it.

"Sounds good, your mum." He put the apple in one of his pockets. "I'll keep it for later."

"Then of course, my mom would skin them, chop them up, and make cider, but the face helped." Rainbow said, casually.

The Doctor grimaced at the possibly gruesome sight, then looked back at the wall. "This wall is solid, and the crack doesn't go all the way through it. So here's a thing: Where's the draft coming from?" He pulled a device out of his pocket, and scanned the crack, as it illuminated a blue light, and emitted a buzzing sound. "Wibbly-wobbly timey-whimey." He said, looking at the small device, before closing it. "Do you know what the crack is?" Rainbow raised an eyebrow. "It's a crack."

Rainbow frowned at that. "How enlightening."

The Doctor frowned, before leaning close to the wall and running his hoof across it. "Alright, I'll tell you something funny. If you were to knock this wall down, the crack would stay put, because the crack isn't in the wall."

"So, where is it?"

"Everywhere." He replied, sounding somewhat confused himself. "In everything, it's a tear in the skin of the world." He ran his hoof along the crack again. "Two parts of space and time that should never have touched...pressed together...right here in the wall of your bedroom. Sometimes...can you hear-"

"A voice?" Rainbow finished, "Often."

The Doctor walked over to Rainbow's bedside and grab the glass of water there, pouring the water onto the floor. He returned to the wall, and placed the glass against it, listening for a voice. "Prisoner Zero..."

"Prisoner Zero has escaped." Rainbow finished again. "I know, I've heard it before. Do you know what it means?"

The Doctor recoiled from the wall. "It means on the other side of this wall, there's a prison. And they've lost a prisoner. And do you know what that means?"

"It means...?"

"You're gonna need a better wall." He proceeded to drag the desk against the wall away from it. "The only way to close the breach is to open it all the way. The forces will revert, and it will snap itself shut. Or..."

"Or...what?" Rainbow asked.

The Doctor pursed his lips. "You know when grown ups tell you 'everything's gonna be fine' and you think they're lying to make you feel better?"

Rainbow glared at the odd stallion in front of her. "Yes."

The Doctor's eyes widened. "Everything's gonna be fine." He extended his hoof, hoping Rainbow would grab it.

Rainbow hesitated. After all, this strange stallion had literally dropped out of the sky, and raided her kitchen, asked her personal questions, and then gave her a bunch of technobabble, hoping she'd understand. She stared into his eyes, and despite his strangeness, she believed him, as though he instilled some kind of trust. Slowly, she took his hoof.

He trotted up to the wall, and activated his device, as slowly, the crack became larger, until it encompassed the entire wall. "Hello?" The Doctor asked, "Hellooo?" With no warning, an enormous eyeball filled the opened, swiveling and turning, examining it's surroundings.

"What the...?" Rainbow asked.

The eyeball continued to stare at them, before sending a beam of energy toward the Doctor's pocket, causing him to fall down, just as the crack snapped shut, and it disappeared.

"There, ya see? Told you it would close!" The Doctor said, with some glee, which was slowly disappearing, "Good as new."

"W-was that...?" Rainbow asked, "Was that Prisoner Zero?"

"No, I think that was Prisoner Zero's guard, whatever it was, it sent me a message." He looked at a small leather wallet. "Psychic paper. Sends a lovely little message. 'Prisoner Zero has escaped.' But why tell us? Unless..." He looked around. "Unless Prisoner Zero escaped through here...But he could've have. We'd know."

The Doctor ran out into the hallway, and looked around, as Rainbow trotted up to him. The Doctor looked down at her, "It's difficult, brand new me, nothing works yet, but there's something I'm missing... something... in the corner... of my eye." He focused on a focused on a door at the end of the hallway, and squinted.

As he took his first step toward it, a loud bell rang throughout the house, distracting him. He looked at Dash, his eyes widening, and on the second ring, he began galloping outside. "No! No, no no no no no no!!!!"

He practically broke down the outside door on his way out. "I've got to get back in there! The engines are phasing, it's gonna burn!" He began fiddling with the grappling hook. Rainbow Dash flew outside, and skidded to a halt next to the Doctor.

"But it's just a box!" Rainbow shouted, confused, "How can a box have engines?!"

"It's not a box," he grabbed the hook, and prepared to throw it over the edge of the box, "It's a time machine."

Rainbow raised an eyebrow. "Really? Come on? You've got a real time machine?"

"Not for much longer if I can't get it stabilized!" He threw the hook into the box, "Five minute hop into the future should do it!"

Rainbow pursed her lips. "Can I come? I mean... could I join you?"

"Not safe in here, not yet." The Doctor explained, "Five minutes. Give me five minutes. Five minutes, and I'll be right back." He hopped up to the box, and prepared to dive in.

Rainbow's gaze fell. "Ponies always say that..."

The Doctor stopped, and looked down. He hopped off the box, and put his hoof under Rainbow's head, raising it ever so slightly, "Am I ponies? Do I even look like ponies? Trust me, I'm the Doctor." He grinned, and trotted back up to the box, and prepared to jump in. He took one last look at Dash, and jumped in. "Geronimooooooooo!!!!!!" The doors snapped shut on the box, and it began to fade in and out of existence, with an almost mystical wheezing sound emanating from it.

As it disappeared, Rainbow flew straight into her bedroom, and packed different items and posters into a suitcase. She hastily tugged on a scarf and a coat, and flew outside, right where the box had been before. She stared at the sky, looking around, waiting for the box to return.

She would wait all night, and longer, unaware of the monster that lurked in her home.

Arc 1, Chapter 3: The Brigadier

The TARDIS dematerialized in the same location, upright this time, in the same location is left. The exited it, coughing. "Rainbow!" He ran toward the house. "I worked it out, I know what missing! You've gotta get out of there!" He used his screwdriver to open the door, and ran up the stairs, and looked at the door to it's immediate right.

He scanned it with his screwdriver, and checked the readings. "Prisoner Zero is here! Prisoner Zero is here! Do you understand me? Prisoner Zero is..." He heard shuffling behind him, and whirled around, as his face met an unfortunate encounter with a gloved hoof, causing him to collapse on the floor.

"...stood, sir. Standing by." A voice finished, as the Doctor awoke. In front of him was a cyan pegasus with rose colored eyes. She was wearing a militaristic uniform, mostly blue, with gold highlights, consisting of many folds and ties. She wore a helmet blue helmet with a lightning bolt on it, and a visor strapped to it, which was pushed up. The mare looked at him. "Alright, unless you want to be injured, lie still."

Ignoring her, the Doctor rushed forward, only to be recoiled back, and have his head get bonked onto the wall behind him. "Oh, that's much better. Brand new me, bonk on the head, just what I needed." He looked at his hoof, and saw that he was strapped to a radiator by a window.

"Alright, hair boy, zip your lips and sit still." The pegasus's eyes frowned. "Why'd you break into this place?"

"You're wearing a uniform, but...wait hold on, hair boy?" The Doctor asked.

"Have you looked in a mirror lately?" The pegasus replied.

"No."

"Now, answer the damn question. Why're you in here?"

"I thought you told me to shut up?"

"ANSWER THE QUESTION, CELESTIA DAMMIT!!!" The pegasus shouted, catching the Doctor off guard.

He shook his head violently, then replied, "I'm looking for Rainbow Dash, is she alright?"

The pegasus recoiled. "Rainbow Dash?"

"Yeah, Rainbow Dash, little blue filly, with a rainbow mane." The Doctor described. "Where is she? I promised her five minutes, but the engines were phasing, I suppose I must've gone a bit far. Has something happened to her?"

"...Rainbow Dash hasn't lived here in a very long time." The pegasus explained.

"How long?" The Doctor asked.

The pegasus stayed silent for a few moments. "A year."

"A year?" The Doctor replied, shocked. "No...no, I can't be a year late, I said five minutes. I promised."

The pegasus glared at the Doctor, anger burning in her eyes.

"What happened to her?" The Doctor asked. "What happened to Rainbow Dash?"

"Brigadier!" A voice from outside shouted.

"Yes, Lieutenant, what is it?!" The pegasus, apparently a Brigadier, shouted back.

"We've checked the perimeter!" The Lieutenant replied, her high pitched voice almost ear-piercing, "Other than this box, nothing appears out of the ordinary."

"Thank you, Lieutenant." The Brigadier replied, and turned back to look at the Doctor.

"I need to talk to whoever lives in this house." The Doctor demanded.

"I live here." The Brigadier replied.

"But you're in the military?"

"And this is my home, you gotta problem with that?" The Brigadier shouted back.

"How many rooms?" The Doctor asked.

This caught the Brigadier off guard. "Huh?"

"How many rooms are on this floor, count them for me now." The Doctor said.

"Yeah, like I'll do that." The Brigadier scoffed.

"Just do it, trust me."

"Why?"

"Because it will change your life."

The Brigadier sighed, "Five. One, two, three, four, five."

"Six." The Doctor finished.

"Six?" The Brigadier said, confused.

"Look."

"Look where?"

"Exactly where you don't want to look, where you never want to look, in the corner of your eye. Look behind you." The Doctor explained.

The Brigadier turned slowly, giving the Doctor a look at her side, and to her tail. "What?" The Brigadier said, "That's impossible, I'd know if that was there."

"There's a perception filter around the door," the Doctor explained, "Sensed it the last time I was here. I should've seen it."

"But, that's a whole room I've never seen before..."

"The filter stops you from noticing," the Doctor said, "Something came here a while ago to hide, and it's still hiding, and you need to unstrap me from this radiator now!"

The Brigadier looked back at him. "Not until I know I can trust you." She started to walk toward the door.

"Don't go toward that door!" He then noticed her tail. It was cut short, in a standard militaristic fashion... and was the color of the rainbow. "You can't be..." He broke out of his trance she he noticed her closer to the door. "Do not touch that door!" She touched it. "Do not open that door!" She opened it. "Oh, Crickey Moses, do I just have a face that nobody listens to!?....again."

She entered the room. Frustrated, he began searching his pockets. "My screwdriver, where is it?! Silver, blue at the end, where did it go?!"

"There's nothing here." The Brigadier said.

"Whatever's in the room, it stopped you seeing the whole room, what makes you think you could see it?" The Doctor said, "Now, please, just get out!"

"Silver, blue at the end?" The Brigadier called.

"My screwdriver, yeah!" The Doctor confirmed, "It must've rolled under the door."

"Definitely," The Brigadier replied, "And then it jumped onto the table."

The Doctor recoiled. "Get out of there," he said, "Get out of there!"

The Brigadier grabbed the screwdriver, which was covered in some kind of goo, then began to walk back toward the door. She felt the fur on the back of her neck stick up. She wasn't alone. She stayed still. Completely still.

"What is it, what're you doing?" The Doctor called.

"There's something else in here." The Brigadier replied, her voice just loud enough for the Doctor to hear.

"Corner of your eye?" He asked, "Do try to see it! If it knows you've seen it, it will kill you!"

"Well, it'll have to try very hard, cause I don't go down easily." The Brigadier replied, prepared to jump what was behind her. She positioned her legs, and with a swift motion, jumped back and kicked the creature in it's face.

It was a long, eel-like creature, connected to the ceiling. It had a blue translucent exoskeleton, and sharp fangs emerging from it's mouth. It saw her, and roared loudly.

"Get out of there!" The Doctor shouted, as the Brigadier came running out of the room. "Give me that!" He said, gesturing to the screwdriver.

"Why?" The Brigadier asked, holding it back.

"Because it you don't you'll die!" The Doctor replied. Hesitantly, the Brigadier gave the Doctor his screwdriver, which he used to lock the door.

"That door won't hold it, you know." The Brigadier scoffed.

"Of course I know, it's an interdimensional multiform from outer space, they're all terrified of wood!" The Doctor said, as he struggled to get free of the strap holding him to the radiator.

The Brigadier looked back at the door, and noticed the door frame was glowing. "What is that creature doing?"

"I don't know...getting dressed?" The Doctor replied, "Just run, get out of here."

"No, this thing has to be stopped." The Brigadier replied.

"Oh, fine!" The Doctor replied, as the door fell over, revealing a stallion with a dog on a leash.

The Brigadier recoiled. "Hold on, huh?"

"Look at the faces." The Doctor instructed.

Sure enough, the creature was growling, but it was coming from the stallion's face. It started to bark loudly, also coming from the stallion's face.

"Okay, that's screwed up." The Brigadier replied.

"It's all one creature," the Doctor explained, "One creature disguised as two, clever old multiform, bit of a rushed job though, got the voice a bit muddled, did you?" The creature focused on him. "Mind you, where'd you get the pattern from? You'd need a physic link, a live feed, how'd you fix that?"

The creature ignored the Doctor, and took a few steps toward the Doctor. "Stop!" He shouted, "You might want to run. She has a lieutenant outside."

"Yeah," the Brigadier supported, "And trust me, you don't want to deal with her, or her sister."

As the creature took another step forward, a voice boomed throughout the house, "PRISONER ZERO, YOU WILL VACATE THE EQUINE RESIDENCE, OR THE EQUINE RESIDENCE WILL BE INCINERATED."

"Ah, there look! More backup!" The Doctor shouted, gleefully.

Prisoner Zero looked around, and entered another room. The Doctor continued to break free of the strap. "Oh, give me that!" The Brigadier used her mouth to break through the Doctor's strap, and grabbed him. She kicked down the window behind her, and jumped out, and landed on the clouds below. "Wait, how can you walk on clouds?"

"I'm not entirely a pony, you know." The Doctor explained, and ran toward the TARDIS, pulling the key out of his pocket, and attempted to open it. "No, no! It's still rebuilding, not letting us in."

The pair heard a barking sound, and looked to see Prisoner Zero from a window. "Come with me, Doctor." The Brigadier ordered, motioning the Doctor to follow her.

"Wait, hold on." The Doctor noticed something behind him. "I destroyed this shed last time I was here, the TARDIS fell on it."

"It was rebuilt." The Brigadier replied, irritated.

"But, it's old, aged!" He licked it. "It's been here at least fifteen years, I'm not one year late, I'm fifteen years late! Why did you say one year?"

"Come on, Doctor, we must leave now!" The Brigadier barked.

"No, this is important!" The Doctor said, "That matters, why did you say one year?"

"WHY DID YOU SAY FIVE MINUTES!?!?" The Brigadier shouted.

The Doctor's eyes widened. "What?"

The Brigadier sighed, and removed her helmet, tossing it to the side, revealing her face and mane. Her rainbow-colored mane was long on the front, drooping down below her muzzle, whilst short in the back, and spiking upward. She has a pink scar over her right eye, and part of her right ear was missing. She had scars on her neck, and any smile on her face was filled with anger. The Doctor then noticed her right wing. It wasn't clad in armor. It was a prosthetic.

"Rainbow Dash..." The Doctor stuttered, "What happened to you?"

"Come with me. Now." Rainbow replied, all seriousness. She grabbed his hoof, and pulled him with her for a few steps, then ran, with the Doctor on her tail. "Lieutenant Pie, report!"

A pink earth pony with a long pink mane ran to Dash's side, "Yes ma'am!"

"Come on, both of you!" Brigadier Dash shouted, "Lieutenant Pie, call your sister! Gaea is under attack, and Cloudsdale is battlefield zero!"

Arc 1, Chapter 4: The Wrong Future

"You're Rainbow?" The Doctor asked, as he, Brigadier Dash and Lieutenant Pie all proceeded down a Cloudsdale street.

"And, you're late." Rainbow replied, a massive frown on her face.

"You punched me in the face!" The Doctor said.

"You broke into my house, Lieutenant Pie and I were the closest ponies in the vicinity." She replied.

"In the face!" The Doctor shrieked.

"And, I'll do it again, so stop you're whining!" Dash bellowed.

The Doctor, taken aback, turned to Lieutenant Pie. "Wait, who are you?"

"Lieutenant Pinkamena Pie," the earth pony explained, "My sister, Maud and I are the leaders of the hundred-and-fiftieth earth regimen."

"Hundred-and-fiftieth?" The Doctor asked, "What happened to the first hundred and forty-nine?"

"Nothing, it's just a good name." Pinkamena said.

"Shut up, Pie." Rainbow said.

"Wait a minute, this is all wrong." The Doctor said, "This isn't suppose to happen, you tow shouldn't be in the military! Rainbow you should be in the Wonderbolts show reserve!"

"Reserve?" Rainbow scoffed, "I'm in the Wonderbolts alright, but I'm certainly not in the reserves. You're talking to Brigadier General Dash, fourth in command in the Wonderbolts Air Force."

"No..." the Doctor said, shocked, "And Pinkie, you're supposed to be cheerful, and a party planner!"

Pinkamena grimaced. "Pinkie?"

"Don't worry about it, Pie." Rainbow replied, "He's just a deluded old horse."

"Deluded?" The Doctor scoffed, "But why would you two be in the military?"

"Why wouldn't we be?" Pinkamena asked, "There's a war going on."

"A war?!" The Doctor said, shocked even further, "What war?"

"The war against the Crystal Empire, idiot." Rainbow said.

"The Crystal Empire?" The Doctor asked, "What did Cadance do?"

"Cadance?" Rainbow asked, surprised, "What the hell does Princess Cadance have to do with this? It's against King Sombra, you dolt."

"Sombra?" The Doctor stopped. "No, no this is all very wrong. This can't be right. This isn't supposed to happen! Unless..."

"Unless what?" Rainbow asked, a steady frown on her face.

"Unless... Rainbow Dash, did you ever perform a Sonic Rainboom when you were a filly?" The Doctor asked.

"That old mare's tale?" Rainbow chuckled, "I wish. I was about to, when I was hit with a spell that caused my limbs to bunch up and stop dead still. I never did figure out who did that."

"It couldn't be..." The Doctor thought for a moment. "Of course, this is the wrong reality! Entering a black hole with a damaged TARDIS must've sent me to a parallel reality, where Rainbow didn't perform the Sonic Rainboom! That's why everything is off! But... what about Twilight? Or Applejack, or Rarity or Fluttershy?"

"Twilight?" Rainbow asked, "As is Twilight Sparkle?"

"Yes."

"I've heard of her, I don't think there's a single pony in Equestria who hasn't heard of her." Rainbow said, sorrow in her voice.

"Why?" The Doctor asked, "Who is she, what does she do?"

"She King Sombra's right-hoof mare." Rainbow said, with utter distaste. "She designed the helmets that force the crystal ponies to fight for Sombra. She's caused the death of countless ponies. Including my brother.

"If I ever get my hooves on that witch, I'll make sure she doesn't take any more lives." Rainbow proceeded forward.

"What happened to your wing?" The Doctor asked.

"Twilight and I have met before." Rainbow explained, "When the Crystal Army invaded Canterlot."

"Hold your ground!" Spitfire shouted at the Wonderbolt Air Force, "They're not getting through our barrier!" They were up in the skies just above Canterlot, staring at the army down below.

"Get ready, stallions!" Shining Armor shouted at the royal guards, "They're coming!" Despite her best efforts to keep the shield up, Cadance was weakening, and the shield could drop at any moment.

The rain was banding on the shield, and the Crystal Army was firing boulders at it.

Rainbow Dash flapped her wings, and looked around. The world was about to explode with violence, and she was right in the middle of it.

"It'll be alright, sis," Rainbow Blitz said, wrapping his arm around his sister, "We'll be fine." Rainbow smiled, not that Blitz could see it, but nodded.

"Alright ponies!" Spitfire shouted, "When that shield goes down we're gonna get poured on! Prepare to adjust your wing power at a moments notice!"

"I can hold them..." Cadance said, looking at her husband, though she was breathing heavily, and was weakening.

"No..." Shining Armor stuttered, looking as a pony walked through the army. She wore a midnight purple cloak with a large, up-turned collar attached to it, a tainted silver crown with a purple, six-pronged star as the centerpiece, and black, crystal slippers. "Twilight..."

Twilight Sparkle's eyes no longer shone. They hadn't shone for years. She walked up to the shield and stared through it. She saw Cadance and Shining Armor looking back at her, comprehending the scenario. She smiled, and closed her eyes. A black aura appeared around her horn, as magical particles appeared around it. Twilight's horn absorbed the particles for several seconds, until it stopped.

Twilight opened her eyes, and smiled cruelly. She then unleashed the power she built up at the shield, causing it to crack, then collapse.

The rain began pouring into Canterlot, as ponies shielded their eyes for a moment. The Crystal Army took advantage of it, and storm Equestria's Capitol.

The battle began.

"CHARGE!!!" Spitfire and Shining Armor shouted at the same time, and the Pegasi and the Royal Guards flew and ran toward the invading army.

They clashed and fought, punching and kicking, hitting and slamming. Rainbow Dash and Blitz fought together, hitting several ponies away. They grabbed ponies, and slammed them into one another. "That one's escaping!" Dash shouted, gesturing to a pony heading toward the throne room.

"Come on!" Blitz shouted, and he and his sister followed the pony.

They cornered him into a wall, and slammed him into it, knocking him down. "He's down," Blitz said, breathing heavily, "Let's get back to the others."

"Oh, my my, is that really the best option here?" A bone-chilling voice said behind the Pegasi, "Let's not be hasty. You haven't fought me yet."

The Rainbow's turned around quickly to see Twilight Sparkle standing in front of them, soaked with rain, and smiling evilly. "Twilight..." Blitz said.

"Oh, it's the Rainbow siblings!" Twilight said, in a cruelly gleeful manner, "You're famous you know! You've fought in so many battles, and won so many! Yet we've still gotten to your capital, and you haven't even scratched the surface of ours."

"Why, Twilight?" Blitz asked, "Why betray your home?"

"Betray?" Twilight chuckled, "I was betrayed! Sombra showed me who I really was, he showed me what I could do with my power, he discovered my untapped potential!"

"How were you betrayed?" Blitz asked.

Twilight laughed. "What, you think I would tell you? I'm not some villain from a comic book, I don't give away my past to the hero. Besides, it's a good thing this isn't a comic book. The hero always wins in a comic book. It's time for a hero to fail."

Blitz had had enough. He charged at Twilight, who merely used her magic to swing him into a wall, where to fell to the ground unconscious. "Rainbow Dash, you've been rather quiet thus far."

"You're going down, Twilight Sparkle." Dash replied, "I'm doing to make sure of that."

"Oh, this'll be fun!" Twilight smiled cruelly, and fired a magic beam at Dash.

Dash leaped into the air, avoiding the magic ray, and came down on Twilight, slamming her into the ground. A black aura appeared around Dash, and sent her flying into a wall, as her helmet flew off. Fortunately, the magic let go of Dash just before she hit it, and she used her momentum to her advantage. She position her hind legs correctly, and swung around, and hit the wall with her hind legs, and boosted toward Twilight, slamming her into a wall.

Twilight swung her head forward, scratching Rainbow's eye, causing her grip on Twilight to loosen. Twilight proceeded to clenched her mouth on Dash's neck, and slammed her into the ground, and then bite her ear, causing Dash to shriek, and then threw her into the corresponding wall, ripping a chunk out of Dash's ear.

Twilight spit out the part of Dash's ear, and then levitated a part of a building and clamped it down on Dash's left wing, causing her to scream in pain. Twilight positioned herself. "Now you fall, Dash. You put up a good fight, but... it's all for not." She began to charge toward Dash, when something grabber her tail, and whirled her into the air, and slammed her into the ground.

"NOT MY SISTER, YOU BITCH!" Blitz shouted, standing triumphantly. He'd removed his helmet, revealing his short cut mane.

"Well, well, well, look who's back on his hooves!" Twilight said, standing up, "Alright then, it won't be your sister. IT'LL BE YOU!!!" She sent a magic beam into him, sending him flying into the wall. He fell onto the ground and stood back up. "Tell you what," Twilight began, "You'll be my new playtoy! Smartypants will be nothing compared to you!"

Blitz flew into her chest, sending her into a wall. Twilight fell onto her hooves, and aimed her horn at him. "Alright, maybe you won't be my new playtoy. I have other plans for you!" Twilight charged toward him, as he braced himself.

Then she disappeared in a flash. "Huh?" He mumble before Twilight reappeared in front of him, and slammed him into a wall, and charged at him at full speed, her horn aiming forward. She him directly in the chest, shoving her horn deep into his chest. She twisted her head a few time, before pulling her horn out, as he fell to the ground, lifeless.

Dash watched in horror as blood mixed with the rain, creating a large red puddle on the ground. "B-Blitz..."

Twilight turned back toward Dash, with a deranged look in her eyes. Her horn was covered in blood, which was dripping in front of her eyes. "Now... it's your turn." Dash struggled to get her wing free from the stone, as Twilight approached her. "Aw, are you stuck? Let me help you with that." A black aura surrounded Dash, except her wing, and pulled her toward Twilight, ripping her wing right off her. Dash screamed in pain, and was dropped to the ground, looking up at her brother's murderer.

"Aw... it's alright." Twilight cooed evilly, "You and your brother will soon be reunited." She aimed her horn.

Dash's eyes widened. Then, a bright light appeared in front of her, causing Twilight to shield her eyes, and when it faded, a tall white alicorn stood there, with a flowing multi-colored mane. "P-Princess...C-Celestia?"

Celestia fired a powerful magical beam at Twilight, who only barely dodged it. "Leave, Twilight Sparkle! Recall your army!" The Princess boomed.

Twilight clenched her jaw. "This isn't the end, Celestia! You'll see me again!" And with that, she teleported away.

Celestia turned to Dash, who was lying on the ground, her conscious fading. The Princess knelt down, and her horn shone. "Rest now, Rainbow Dash. You've gone through enough for one day."

Rainbow felt drowsy all the sudden, and collapsed. "General Spitfire!" Celestia shouted, loudly.

On cue, Spitfire flew it, displaying a torn uniform and several cuts and bruises. "Yes, Your Majesty!"  The General then noticed the fallen pegasi. "No... Rainbow..." She landed on the ground.

"Rainbow Dash is alive, but injured. She must be taken to a medical facility at once." Celestia explained, "Sadly... Blitz... he didn't make it."

"No..." Spitfire mumbled, looking over to the impaled pegasus.

"We've lost this battle." Celestia said, remained serene, despite the chaos around her, "We must retreat."

"But... " Spitfire began, "Your Highness, we can still win this!"

"NO!!" Celestia boomed, "Enough blood has been split this night! Use the caves beneath the city, evacuate to Ponyville!"

Spitfire regained her composure. "Yes, Your Majesty!" She took off. "Lieutenant Rift! Prepare an evacuation!"

Celestia levitated Rainbow Dash onto her back. "Come, Rainbow Dash. We must get you out of here." Her horn shone, and she teleported away.

Rainbow Dash awoke some time later, lying in a small tent. Everything was hazy, and fuzzy. There was a steady sunlight beating through, that felt calming in a way. She started sitting up, when she was suddenly stopped by a hoof, which gently lied her back down. "Easy there, sugercube," a female voice said, with a deep southern drawl, "You've had a hell of day. Just rest. I'll get you some cider, and you can sleep."

Rainbow's eyes felt stuck shut. She attempted to stay awake, but she simply couldn't. She drifted off...

Rainbow awoke again, this time sitting up instantly. "You're awake." A young voice with a southern drawl said, "Here, take this." Rainbow's eyes slowly opened, and saw a small light yellow filly with a red mane, holding a glass to Dash. She wore a tan jumpsuit, with her mane and tail each in a hairnet.

Reluctantly, Rainbow took the glass, and took a small sip. Warm apple cider... Rainbow's favorite drink. It was either a strange coincidence, or intentional. "T-Th-Thank Y-You..." Rainbow stuttered, before taking another sip of cider.

"You're very welcome." The filly smiled, and nodded.

"Applebloom, " the same voice from earlier said, "Go and take care of some of the other patients. I got the Captain here." The voice belonged to an orange mare with green eyes, and a blonde mane and tail. Like the filly, apparently named Applebloom, the mare wore a tan jumpsuit, though hers had several stains, and her mane and tail were in hairnets.

Applebloom, nodded and left, with her head hanging. "Don't mind 'er, she jus' wanted to see you 'wake, is all." The mare walked up to Dash, "The name's Applejack. You doin' alright? I don't think you would be, considerin what you've been through."

Rainbow grasped for words. "Wh-Where am I?"

"The Apple Mill, jus' outside Ponyville, or what used to be Ponyville," Applejack explained, "After retreating from Canterlot, y'all came here to recuperate."

"W-We lost?" Rainbow asked, shocked.

"'Fraid so, sugercube." Applejack replied, with sorrow in her voice.

Rainbow's mouth gaped for a while, before closing and swallowing. "I...I... I want to see my brother."

Applejack looked on, sadly. "Alright. I'll help ya down." Applejack walked over to Dash, and helped her climb over the edge of the bed, and onto the ground. "A'm gonna let go of ya now, alright?"

Rainbow nodded, and Applejack let go of her. She suddenly felt a loss of balance, and she extended her wings to maintain her balance, but then she felt heavy to her right. She looked over to her left side, and was shocked by what she discovered. Where her wing should be was a bandage with a red hue to it. None of her wing remained.

She swallowed heavily, and let out a small sob. She attempted to walk forward, and fell over for a second. "You okay?" Applejack asked. Rainbow nodded, and stood up, her legs wobbly. With determination, she proceeded forward, and exited the tent.

It wasn't sunny outside. It was overcast, with many ponies bustling about, but not in a cheerful way. Nopony was happy, nopony had smiles. They had lost the battle, and they must've had casualties.

Rainbow Dash limped on her left side, but proceeded forward. "Captain Dash!" A voice called. Dash turned to see a black and red pegasus running toward her.

"S-Shadow..." Rainbow replied, and she limped to him. Shadow Rift was a Second Lieutenant, and was exactly two ranks below Dash. Unlike most of the military, he had actually met King Sombra, and had a darkened eye as a result.

"Are you alright, Captain?" Shadow asked, minor panic in his voice.

"I-I've been better." Rainbow said, "You? Still following that cellist around?"

Shadow blushed. "No, she left some time ago. I'm not sure where." He sighed, "Oh well, I shouldn't dwell on the past. Besides, I have a duty to perform, for all of Equestria."

Rainbow nodded. "Duty isn't everything, Shadow," Rainbow said, "You have to think about family too. Speaking of which, where's Blitz?"

Shadow's face fell. "I think you outta talk with General Spitfire." He said, sadly, and pointed toward a nearby tent.

Rainbow looked at the ground, then walked toward the tent.

Spitfire and Celestia were inside, as if they were waiting for her. "Rainbow Dash... I'm so sorry."

Rainbow looked at them, confused. "Where's Blitz?"

Celestia took a step toward Rainbow Dash. "I am deeply sorry, Captain Dash. This will come as a shock."

Celestia took a step back, as did Spitfire, to reveal Blitz lying on a bed, lifeless. He had a massive wound in his chest, with several other wounds along his body. "Blitz... no..." It all came back to Dash at once. The battle against Twilight, losing her wing, losing her brother.

"Oh... Blitz!" Rainbow burst into tears on Blitz's body. She wept, and wept, covering Blitz's fur with her tears. "Oh, Blitz! I'm so sorry!" She sobbed through the tears, "I couldn't save you! I swear, on my life, you will be avenged!"

"It was all we could do, Captain." Nurse Redheart said, looking over Dash.

Rainbow stood up, flexing her new prosthetic wing. It didn't feel right. Her actual wing had felt natural to flex and move, this one just felt... wrong. "It'll do." She groaned. She folded it up, and began to walk.

"Rainbow Dash, I have a new assignment for you!" A voice greeted her as she left the medical tent. Spitfire walked up to her, her face stern.

"Yes, General." Rainbow Dash replied, standing attention.

"At ease, Captain." Spitfire said, allowing Rainbow Dash to loosen up. "I'm assigning you with the Pie sisters, Pinkamena and Maud. You're going stop any small advances. Our intelligence tell us that small groups of ten or less Crystal ponies are advancing in our borders. We're sending small strike teams to deal with them. You three are going to the Crystal North to stop some."

"Yes, sir." Rainbow Dash nodded, "Anything else, sir?"

"One more thing, Dash." Spitfire said, "You're being promoted. You are now a Major in the Equestrian Wonderbolt Air Force. Congratulations."

"Thank you, sir."

"Colonel!" Shadow Rift shouted, flying toward Rainbow Dash.

"Captain." Rainbow replied, "Good to see you."

"And you, Colonel, or should I say Brigadier General." Shadow replied, "You've come a long way, haven't you?"

"Some say I have, I'm not so sure." Rainbow replied, humbly. "Shadow, your leg..." Dash said, eyeing Shadow's left foreleg.

"Oh, it's a prosthetic, kind of like your wing." Shadow said, looking at Dash's own prosthetic. "Although, mine is more advanced."

Rainbow frowned, "How humble."

"Oh, don't worry, Colonel," Shadow comforted, "I'm sure they'll upgrade yours soon."

"They'd better not." Rainbow said, angrily.

"What do you mean?" Shadow asked.

"It may have been easy for you to get accustomed to your prosthetic, Captain, but it wasn't easy for me." Rainbow replied.

"Rainbow, it was two years ago..." Shadow said.

"That doesn't mean a damn thing!" Rainbow shouted, "I just got accustomed to this thing, I don't want a new one. And remember: You lost a leg. I lost a wing. I used to fly most of the time, I was never on the ground. Now look at me. Even with this prosthetic, I can't fly like I used to.

"Two years ago I lost a lot. Not just my wing, but my brother as well. I've lost a lot, Shadow, I don't need you criticizing me." Rainbow began walking away. "You'd better get to the ceremony. I don't think I need one, but Spitfire insisted. See you there." Rainbow stormed off, leaving Shadow to ponder her words.

"Rainbow, what is it?" The Doctor asked.

"Huh?" Rainbow mumbled, being broken out of her trance, "Nothing, just recalling a memory..."

Arc 1, Chapter 5: Locate

"Hang on, we're not scheduled for clouds." Rainbow Dash said, as the sky began to darken. She looked up, and saw no clouds, but the sun itself going out. Part of light returned, but the sun was masked, as if looking at it through stained glass.

"What happened to the sun?" Pinkamena asked, looking up.

"Nothing, you're just looking at it through a force field," the Doctor said, "They're sealing off the atmosphere, but why would they do that? Unless..." The Doctor trotted to a street side, gazing around. "Of course, they're getting ready to burn the planet." The Doctor turned grim.

Brigadier Dash turned to the Doctor and grabbed him by the collar, "What do you mean, 'burn the planet?'"

The Doctor wriggled loose of Rainbow's grip and began explaining, "The equine residence, it wasn't talking about your house, it was talking about the planet. The Atraxi are going to burn the planet unless they get Prisoner Zero back in custody."

"Great." Rainbow said, "You know everything else, do you know how much time we have?"

"Let's see," the Doctor began, "Two poles? Basic molten core, that'd require a setting eleven fissure blast, how long would that take to charge up? Twenty minutes? Yeah, that sounds right. We've got twenty minutes."

"So, twenty minutes to save the world from an alien race?" Rainbow asked.

"Yep." The Doctor confirmed.

"Well, it's a nice change of pace from King Sombra's army." Rainbow said, "You have our support. What do we need to do?"

"Well, for starters, we need to locate Prisoner Zero," the Doctor explained, "Then we need to get the Atraxi's attention, then have them see Prisoner Zero, then they'll take it. After that, we should be good."

"I know how we can find Prisoner Zero." Pinkamena said, getting the other's attention.

"How's that?" The Doctor asked.

"My sister, Maud." Pinkamena replied, "She has great tracking skills, and should be able to find anypony no matter what."

"Great, how we summon her?" The Doctor asked.

Pinkamena smiled, and pulled out a whistle from her uniform, brought it up to her lips, and blew in it... which resulted in no noise whatsoever. "Uh... Pinkamena, I think it might be-"

He was cut off as a grey pony with a short purple mane and blue eyes quickly stepped in front of him. She wore the same uniform as Pinkamena. "Everypony, this is my sister, Maud."

Maud turned around, saluted Brigadier Dash, and just looked at the Doctor, then turned to her sister and gestured to him.

"No, he's not in the military," Pinkamena clarified, "He's a... consultant, for this particular mission."

Maud nodded, and made several more gestures to the Doctor. "No, he's not a spy for King Sombra. At least, I hope he isn't." Pinkamena turned to look at the Doctor, "Are you?"

The Doctor inhaled, "Um, no."

"Alright, he isn't a spy." Pinkamena told her sister. Maud made more gestures. "Maud says that she doesn't trust you, but if you're working with us, then she'll obey what you ask of her. But it will take a while to earn her trust."

The Doctor cocked his head to the side. "Doesn't she talk?"

"It's hard to talk without a tongue." Pinkamena replied, as her sister turned to the Doctor and opened her mouth wide, allowing the Doctor to look in.

"Huh." He said, seeing that there was no tongue, "I bet there's an interesting story behind that."

"There's an 'interesting story' behind all our wounds," Rainbow Dash replied, gazing at her prosthetic wing, "But, right now, we need to find Prisoner Zero. Maud, do you think you can find them?"

Maud nodded, and gestured to the east, and began running in the direction, stopping only once to signal the others to follow.

Maud jumped atop a hill, and pointed down. The others joined her, and saw that she was pointing at a colt with a dog. "There's Prisoner Zero." Pinkamena stated, "What's the plan of attack?"

"I'll fly down there and tackle him, then we'll signal the aliens, and have them come get them." Rainbow said, looking forward.

"Oh yes," the Doctor said, "Fly down and tackle the carnivorous multiform, and try not to get killed, yes that's a brilliant plan!" The Doctor sighed and shook his head.

Maud turned toward him and made several signs and gestures with her hooves. "Maud asks if you have a better plan." Pinkamena asked on behave of her sister.

The Doctor smiled. "I do." He looked over to the multiform. "The Atraxi are searching for a being from outer space, so they'd probably be searching for something nonequine. For example, technology." The Doctor reached into his pocket and pulled out his sonic screwdriver. "If this isn't nonequine, I don't know what is."

"What are you suggesting?" Rainbow asked.

"If we get close enough to Prisoner Zero and activate the sonic screwdriver, then the Atraxi will be drawn to our position, then we need to figure out a way to tell them what Prisoner Zero is."

"And how do we do that?" Pinkamena asked.

"We need to draw Prisoner Zero out into the open; make is revert to it's original form." The Doctor explained.

"And do you have a plan to do that?" Rainbow asked.

"No idea." The Doctor replied, and began his trek down the hill.

Pinkamena stood next to Dash. "He's just making this up as he's going along, isn't he?"

"I guess so." Rainbow replied, "Odd thing is, he's pretty good at it."

"Prisoner Zero!" The Doctor shouted, trotting up to the fake pony with a dog. "Remember me? You tried to kill me about ten minutes ago."

"Doctor, you're stalling!" Rainbow shouted, who was flying above them.

"Oh, right sorry." He pulled out his sonic screwdriver. Prisoner Zero, you know what this is? It's a sonic screwdriver. Your cell guards are looking for nonequine technology, and nothing says nonequine like a sonic screwdriver!" He raised it up, and activated it.

The sonic waves began to shatter windows around them, and activate certain technology. "I think someone's going to notice, don't you?" As he spoke, and Atraxi came flying in, it's enormous eye swiveling.

Rainbow looked at it. "Whoa..." She wasn't often surprised.

"Well, Prisoner Zero, it was nice knowing you!" The Doctor said, "Send me a postcard from prison!" Just then, his sonic screwdriver exploded above him, showering him in sparks. He dropped the remains of it quickly. "No, no! Don't do that!"

The Atraxi looked away, as Prisoner Zero escaped. "Wait, Prisoner Zero is here! Prisoner Zero is...here." The Atraxi was gone. Rainbow, Pinkamena and Maud joined the Doctor on the ground.

"Prisoner Zero is gone." Pinkamena observed.

"Well of course it is!" The Doctor groaned. "No TARDIS, no screwdriver, eighteen minutes to save the world. How am I gonna pull this one off?"

"Hold on," Rainbow said, "When Prisoner Zero first transformed, you said he needed a physic link, a live being to get the image from."

"Oh yes, of course!" The Doctor exclaimed, "Rainbow Dash, you're brilliant! Prisoner Zero would need time to set up a physic link. It would render a pony unconscious while it set it up, and took the image. It would look to everyone else that the pony it took the image from was under a coma. And, knowing a race like Prisoner Zero, it would've tried to get multiple images, thus more comatose patients. Rainbow Dash, is there anywhere in Cloudsdale that might have several comatose patients?"

"There's the hospital near the Wonderbolts headquarters. Several patients were committed about seven months ago." The Brigadier replied.

"Alright, you go on ahead, I have something I need to do before I go there." The Doctor replied, giving Rainbow a little push.

"Like what?!" Dash shouted, angrily, "What could be more important than saving the world?!"

"Doesn't matter, just go!" The Doctor replied, as he began running in the opposite direction.

Rainbow Dash rolled her eyes and groaned. "C'mon, let's go." She extended her wings and bolted into the sky.

Prologue

The Equestrian Doctor took one final look around his TARDIS. After all, it was the last time he'd see it with these eyes. Possibly with any eyes. He stepped in front of the console, and gazed at the view monitor. He was roughly a minute from the sun.

He stepped around the console, and looked at the door. He gazed down at his hand in front of him. It was glowing, and energy was starting to seep from it quicker, and quicker.

He looked up, and faced the TARDIS wall, as if there was someone standing there. And, as the energy began to seep from his neck up, he chuckled, and muttered, "Allons-y...."

He inhaled sharply, and his arms and legs extended, as golden energy seeped out of them at a massive rate.

The TARDIS entered the sun, and it's windows exploded, and the interior caught fire in certain places. It shook violently, and part of the supportive structure fell apart, smashing onto the ground.

As the TARDIS roared and shook, and as the regeneration energy started to fade, the Doctor screamed.

"AHHHHHHHH!!!!!!!!!!!!!!!!!" The energy vanished, and the new Doctor stood there.

The TARDIS suffered a massive jolt, and the Doctor whirled around, and looked down. "Legs! I've still got legs!" His kissed his left leg. "Good!"

He felt his arms. "Oh, arms, hands! Ooh! Fingers, lots of fingers!" He grabbed his ears, "Ears: Yes. Eyes: Two. Nose? I've had worse... Chin!" -he felt his chin- "Blimey... hair!" He ran his hand through his hair, and felt the length of it. "I'm a girl! No!" -he grabbed his throat, and his voice got deeper- "No... I'm not a girl." He pulled his bangs down in front of his face, "Oh, and still not ginger!" He began tapping the side of his head. "But, I'm forgetting something important... I'm... I'm I'm I'm..." the TARDIS shook violently, and he grabbed onto the console, and laughed. "Ha! Exploding!"

The New Doctor maneuvered around to the console monitor, and stared at it. "Let's see.... the revert hasn't started yet, so..." He adjusted the scanner, "Ah! A black hole! Chances of survival, limited, but hey! What's life without risk?!" He maneuvered the TARDIS into the slightly forming black hole. "Ah! Ah ha ha!"

The TARDIS entered the black hole, and the Doctor shouted gleefully, "GERONIMOOOOOOOOOOOOOO!!!"

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