Doctor Whooves: An Equestrian Invasion

by Weeping Angel

Rating: everyone
Tags: Crossover, Alternate Universe, Dark, Comedy, Adventure
Length: 4246

New body, new planet, old enemies. What could possibly go wrong when the Doctor is sucked into Equestria?

When the eleventh Doctor regenerates in his TARDIS, he is excited to see the new body he has manifested into.
And when he meets an some ponies who truly appeal to him, making him remember all of his fun times with his old companions.
But he isn't the only Time Lord to have regenerated into Equestrian form. The Master, archenemy of the Doctor, appears as well, younger then when he died but yet hating him as much as ever. After he discovers the Doctor's presence in Equestria, the Master will do anything to destroy him. Even if it means pairing up with Discord.
And Daleks, there are Daleks too.

***This is an alternative to the whole "Trenzalore" gig. This takes place after the Day of the Doctor and replaces the Time of the Doctor***

Published 1970-01-01 00:00:00 UTC
Last updated 2013-12-26 19:20:03 UTC

Part One: Change

Part One

Change

The Doctor pulled a lever on his TARDIS, sighing contentedly. It was a fun four days with his beloved companion, Clara Oswald. They went to Mesopotamia and met King Sargon II (terrible bloke, the Doctor thought) and stopped an incurring invasion of Daleks.

No, time was not on his side anymore. His time was almost up, and he would most likely never see Clara again.

He hoped he wouldn't cause her too much pain.

The Doctor sat back on the chair a few feet away from the console. Suddenly the TARDIS was filled with a chiming noise coming from the clock a few meters away.

12 o'clock.

Any time now, the Doctor would regenerate. His eleventh form was fun, and it would not be forgotten. He just hoped the memories of Clara wouldn't die along with the body.

Or of Amy.

The Doctor shook back tears. How long had it been since the deaths of his best friends, Amy and Rory? Years and years. And yet he still had tears when he thought of them.

The clock chimed again. The TARDIS was reminding him of his oblivion.

"I know, girl. I know," he told her absentmindedly.

Suddenly the Doctor was jerked from the seat, and sent flying into the console. The TARDIS was in flight.

"Wh...where are you going?" he asked her. The TARDIS, as always, did not answer.

The Doctor's gaze inched towards his hand, which was glowing with a familiar gold hue.

It was time.

The TARDIS continued its flight, not stopping for the Doctor's moment.

His entire body lit up with the gold, consuming his features entirely.

"I...I don't want to go," he said, tearing up. "G...geronimo."

Then the gold dust consumed him entirely, and his hands shot up, the gold flying around the TARDIS. He screamed in agony.

~~~~~~

The Doctor collapsed on the ground, his regeneration complete, just as the TARDIS landed.

"Whew!" he told no one in particular. But something was strange. He sounded just like...just like his tenth regeneration.

Weird.

The Doctor stood up, and almost instantly fell over again. His head was spinning, and he couldn't see properly. He decided to go on all fours, which worked perfectly.

Then his eyesight worked again, and he looked down. Gasping, the Doctor fell over, completely put off. His hands...weren't hands. They were...hooves?

Was he a...pony?

The Doctor had heard of these, of course. They lived on the magical planet called Equestria, which the Doctor had refrained from visiting.

Was he really one of them?

He looked at his rear (flank?) and suddenly his suspicions became a reality. A "cutie mark" adorned it, depicting an hourglass.

Using his hooves, he touched his hair, happy that just like his voice, belonged to his tenth regeneration. Then his hooves wandered to his bow tie, and with a sad look, he dropped it on the ground.

Bow ties were no longer cool.

The Doctor gingerly walked over to his closet and pulled out something he thought he would never wear again.

His trademark suit and long coat.

After a few minutes trying (and failing) to put on the coat, he shed it somberly and instead put on the blue suit instead (only the coat part though, the pants couldn't fit), remembering to add the necktie.

Checking himself out in the mirror, the Doctor concluded that he looked like a pony-fied version of his tenth regeneration. Sitting down, he felt a crunch in his pocket which turned out to be none other then his glasses. He put them on the bridge of his snout.

The TARDIS console "ding"-ed, and the Doctor trotted over to it, a smile adorning his face.

The TARDIS had granted him a pony-sized sonic screwdriver, identical to the one he had in his tenth regeneration.

After he picked it up, the Doctor decided it was his moment of truth. His hoof pushed away the TARDIS door, welcoming him to the outside world.

Equestria.

~~~~~~

The Doctor fell out onto the dirt, face planting. He picked himself up, dusted himself off, and stepped into the bustling pony area.

"Watch where you're going!" an obnoxious colt shouted to him, veering the carriage he had behind him. The carriage toppled over on its side, bringing the pony down, too.

"Oh, buck!" he said, frantically trying to unhook himself from the brace.

From inside the carriage, a pony groaned. "Ugh, my head hurts."

With a flap of something that sounded like wings, the pony lifted herself from the carriage. Her coat was gray and her mane was blonde. But what the Doctor thought was most weird were her eyes. They were both facing different, wacky directions.

"Oh, great," she said. "I just got those fixed."

She looked at the Doctor (er, he thought she looked at him. With her eyes, he couldn't really tell.) and flew over to him. "Hi, there," she said. "My name is Derpy Hooves. What's your name?"

She didn't mention anything about the grumbling colt trying to save his carriage or the carriage itself falling on her.

"I...I'm the Doctor," he replied.

"Doctor? Doctor Whooves?"

"Actually it's..." the Doctor paused for a second. Weird new alien body, weird alien name. "Yeah. That's about right."

"Hey, miss, mind lending me a hoof?" asked the colt.

Derpy tossed him some bits. "Here you go, twice what you asked for. For your troubles."

Then she landed close to the Doctor and looked in his eyes (or at least he thought it was his eyes. Like he said, you couldn't really tell).

"So, what's your story?" Derpy asked him.

"My...my story?"

"I know every pony in Ponyville. And I've never seen you around here." She paused for a second. "Wait...I don't know everypony in Ponyville. That's Pinkie Pie."

The Doctor stared incredulously at the mare with an identity crisis.

"I know! I'll bring you to Pinkie Pie!"

Derpy Hooves grabbed the Doctor and lifted him up, flying about five feet in the air. His hooves dragged across the ground.

The Doctor sighed.

~~~~~~

In another corner of Equestria...

The Master sighed as he broke apart yet another rock.

Over the past three years, he decided one thing.

Rock farms were boring.

Suddenly the farmer called time, and the Master dropped the bucking rocks that he had been working on for the past eight hours, running to the farmer.

"How many rocks did you do today?" he asked in monotone.

"Five thousand and twenty-three," he replied, gasping for air.

"Hm. Good job, kid."

"Yeah, yeah. What's pay for today?"

The farmer looked nervous. "Um, well..."

"What?"

"Pay has gone down. Rocks just aren't as valuable like they were a few months ago."

The Master's anger grew. "You're...telling...me...I...just...worked...on...bucking...rocks...for... EIGHT BUCKING HOURS JUST TO GET MINIMUM WAGE?"

"Well, yes."

"But I'm your ONLY EMPLOYEE!"

"Yes, so you get more money, then say, if you weren't the only employee."

The Master grabbed the bits in the bag the farmer was holding out for him, and said, "I QUIT!!!"

The Master ran back to the hotel he was staying in, not listening to the farmer yell behind him, saying 'how much he needed him' or 'hey! I'm not paying you to run!' Instead, he was thinking about the key to his room he had lost a few hours before. In the midst of his rock-breaking, a crevice had appeared, where the key had slipped from his satchel.

The hotel where the Master was staying in was terrible. It's walls sagged, cracks showed, and rats ran around everywhere. But he hoped it was kind enough to give him another key.

He walked up to the receptionist, who stared blankly at a magazine.

"Excuse me," the Master asked the receptionist. "But, um, I lost my key."

"That ain't my problem."

"But you run this place. I need another key."

The receptionist looked up at him with blank eyes. "Well, ain't nothing I can do for ya, cupcake. You lose the key, you lose the room."

"That's a terrible quote!"

"Well, it's what you're getting."

"Can I at least get my stuff back?"

The receptionist smiled. "Already sold 'em on eNeigh."

The Master gritted his teeth. "I'm pretty sure that's illegal."

She shrugged. "You shoulda read the ratings of this bucking hotel, idiot. Everything we do is illegal, but nopony bucking cares about this dump."

The Master sighed, tears welling up in his eyes. He had left his laser screwdriver in the room. He loved his laser screwdriver.

Anger boiled inside of his equine body, reaching his tipping point. Amazingly, he withheld the anger until he reached the outside, spilling it all out.

"AaaaHHHhh!" He yelled, oblivious to the staring ponies bustling around him.

The Master hung his head, and started walking away.

A few hours later, the Master wandered away from Trottingham and walked through a forest.

Finally, he came across a tree house where he had made camp a few weeks ago. The food and things he had left there were still piled up on the floor.

He flew up to the top of the tree and looked beyond. Trottingham was beginning to turn out the lights, and go to sleep. Maybe he should do the same.

The Master flew down now, and curled up on the bed sheets that were splattered out on the floor. Tomorrow he would go find another job, even though he doubted the overpopulated city of Trottingham would have anything available. But it was his only chance.

As he lay there, his body was overcome with a strong sadness, and at that moment he remembered the red fields, tumbling suns, and beautiful skies of his true home; Gallifrey.

Despite what all the Time Lords say, the Master loved his home planet. Sure, he was a "rogue" Time Lord and all that jazz, but would he ever forget his favorite planet?

At that moment, the winds thickened, blowing a strong breeze into the tree house. The Master flew over to the doorway, which was covered by a sheet, flying in the wind.

"Well, then, what do we have here?"

The Master whipped around, studying the shadows in the tree house. "Who's there? Show yourself!"

A laughter erupted in the room, and a pair of eyes glowed in one of the shadows.

"Don't worry, Time Pony. I'm here to help."

The Master grunted in reply. "I'm not afraid of a voice and a pair of eyes. I've fought Daleks and Time Lords, more then you'll ever be."

"Oh? And how would you like to meet the master of chaos, the new emperor of the Daleks?" The voice materialized into a big lumbering body, equipped with what looked like a jumble of animal bodies smashed together. He laughed. "My name is Discord, and as you probably have noticed, I'm not pony. No, but I can help. Do you know how long it took me to find a Time Pony who could appreciate my offer? Decades, I tell you! And it got me turned to stone! Not much leg room there."

The Master was confused. "What offer?"

"Why, for us to be partners! Master of chaos, master of time, we're good! And together, we can destroy them once and for all!"

"Them? Who's them?"

"Well, I know a pony by the name of the Doctor," Discord mused. "He just regenerated. Perfect for destroying. But what I want is different." He paused for a second, and cleared his throat. "I've been wanting to do this for ages. For me, what I want to do is destroy Princess Celestia and capture Princess Luna."

The Master stepped back, considering the offer. "Why capture Luna and kill Celestia?"

"Because I hate her guts, and when my-ahem, our- empire rises, I want Luna by my side as my...wife, I suppose. She is a good ruler." Discord chuckled. "And beautiful."

The Master smiled. He was liking this "plan" of Discord's. "Okay. I'm in."

"Excellent!" Discord flew up, clapping his paws. "Now, all you have to do is sign a contract saying that you agree to my terms." A packet of papers and a pen appeared in Discord's paws, and the Master eagerly took it.

~~~~~~

The Doctor was pushed into a room surrounded with ponies.

"Derpy, who is this?" asked a cyan pegasus with a rainbow mane.

"Oh, this is the Doctor," she replied, pushing him towards the pegasus. "I've come to bring him to Pinkie."

Suddenly a pink one bounded up to the Doctor, and started bouncing up and down. "Ooh! That's me! Yay, you want me!" She giggled and toppled over, causing more giggles.

"Why in the world do you need Pinkie Pie?" The pegasus asked again.

Derpy smiled, opened her mouth, then closed it again. "Actually, I don't remember."

The Doctor sighed, and started walking out the door.

"Hold on there, mister!" Pinkie Pie shouted to him, who had since then gotten up off the floor. "We only just met! And when I meet a pony, the first thing I want to do is throw a PARTAY!"

Pinkie Pie blew a horn that sounded all over the city. Suddenly, floods of ponies blundered into the house, shouting and whooping in delight. Apparently, the pink earth pony's parties were something very popular.

Soon enough, a purple unicorn foal walked over to Derpy and poked her.

"Excuse me," Derpy told the Doctor, and she walked away from him with the foal. Strange, she seemed very wound up, looking at her.

The Doctor decided not to push it, and instead almost ran into a unicorn, this time not a young one. A mare, teenage, by the look of it, slammed into him, her bright blue mane sticking up everywhere.

"Whoa, there, friend!" She said, her dark glasses covering up her eyes. "Didn't mean to bump into ya. Sorry, I didn't see where I was going, there."

"No...no problem," the Doctor replied.

The unicorn trotted off, running to get some speakers or something.

Pinkie Pie walked up to the Doctor. "Great party, huh?"

"It's really something."

"Yeah, well, we're gonna have another party tomorrow. Do you wanna come?"

The Doctor smiled, deciding it was time to make some friends. "Yeah, great! What's the occasion?"

Pinkie laughed. "Oh, you're such a silly-billy! Tomorrow's Night Mare Night! And guess what? Princess Luna's coming here to Ponyville again! It's going to be soooo much fun!"

Princess Luna? The Doctor never heard of her. But she seemed nice, unlike the "Night Mare Night'' Pinkie Pie was going off about.

After a few hours of partying, where the Doctor was greeted with many different ponies, the guests all returned to their homes, stomachs bulging and spirits high.

"Don't forget about tomorrow!" Pinkie called to them, and they all "hoorah"-ed.

~~~~~~

The Doctor wandered outside, content to the bone. Pinkie's party really was fun, and he was glad to have gone there.

He unlocked the door to his TARDIS and stepped inside. The machine purred in content.

"Hey, there, girl," the Doctor soothed. His hoof went to the console, and he started the machine.

One last visit to Earth. One last time before he would have to go away, and live on Equestria. One last time...

"Whatcha doin?"

The unicorn foal sat on the console, staring down at the Doctor. He screamed.

"Oh, don't be such a wuss."

"How did you get into my TARDIS?"

"The blue box? Oh, it was unlocked."

"Unlocked?" The TARDIS was always locked, and never let anybody in without the key or the TARDIS's favor.

"Yeah. Anyway, I was just here to tell you Mom says that you can stay with her tonight, but by the looks of it, you have plenty of bunk beds to sleep on. So, I'll just go back to Mom now."

The Doctor was frazzled. "Mom?"

"Yeah, the gray pegasus you were talking to. I'm her foal."

The Doctor stepped back. Why would Derpy look wound up if it were her daughter? Ponies were weird.

"My name's Dinky, by the way. Dinky Hooves."

"Okay, then Dinky Hooves. Get out of my TARDIS."

Dinky scoffed. "Mom said you were going to be nice."

"I just don't want you in here! Do you know what would happen if you pulled any of these levers?" The Doctor said to her, exasperated.

"Oh, you mean, like this?" Dinky smiled treacherously and pulled the lever that mainly just controlled the toaster in the kitchen (what? He gets hungry!)

Then the Doctor got an idea. "Oh no! That lever that you just pulled was the self-destruct!"

"What?!"

"Get out of here while you can!" The Doctor frantically ran around the console, pressing random buttons that he knew would do no harm.

Dinky sprinted off, slamming the door behind her. She was wailing all the way.

The Doctor was not here to make friends.

He abandoned the console, adding one last tap, and shifted on out to get some sleep in the bedroom.

The bedroom that had once belonged to Amy and Rory.

~~~~~~

The nightmares came back.

The Doctor could feel the terror he had felt before.

Doctor? Oh, Doctor?

No. He must not listen to the voice.

Oh, Doctor. Do you not like me anymore? Has our friendship been destroyed?

That voice, though. Which one did it belong to? Was it Rose Tyler, or Martha Jones? Each night, a different companion would haunt his dreams, terrorizing his thoughts, making him remember all the bad things he had done to them.

Doctor, do you not remember me? I thought I was the Impossible Girl, does that mean nothing now? How I saved you from the Great Intelligence, year after year, form after form?

"No, Clara. I haven't. Please, forgive me."

Why should I forgive you? You abandoned me. Threw me away. It's Wednesday now, Doctor. Keep up.

"A Wednesday," the Doctor mumbled.

What? What do you have to say to me now?

"I didn't say next Wednesday, I said A WEDNESDAY!"

~~~~~~

The Doctor willed himself awake, only to be met by a pony standing over him.

"Hey, silly-billy!" Pinkie Pie greeted him.

The Doctor groaned.

"You slept for a looooong time!"

"I know."

"Well, you almost forgot about Night Mare Night!"

The Doctor jerked up. "It's nighttime?!"

Pinkie laughed in return. "No, silly-billy! Night Mare Night lasts all day. Normally, it's 9:00 AM."

The Doctor groaned again.

"So, I'm here to bring you to the PARTAY!"

Shaking his head, he replied, "Is the princess here yet?"

"Of course! She's with Rainbow Dash and Derpy in the main hall, getting ready to make a speech at twelve."

Pinkie Pie pulled the Doctor out of the bed, accidentally slamming his head on the floor.

He managed to scramble out of Pinkie's grasp, grabbing his glasses and sonic screwdriver. Then he followed the party pony all the way to the main hall, waving to ponies he met yesterday.

When the two got to the main hall, Pinkie pushed open the door.

"And I would like to introduce you to the Princess of the Night, Princess Luna!"

The Doctor's eyes widened. Princess Luna stood with the two pegasi he met yesterday. She was a unicorn-pegasus, and was levitating three different scrolls, intently reading all of them. Her mane was a misty, sort of wavy thing, and her coat was a beautiful shade of midnight blue.

Upon his arrival, the princess leaned down to Rainbow Dash's level and whispered, "should I use the Royal Canterlot Voice?"

The rainbow mare shook her head.

"Oh, um, hello. I'm Princess Luna." The mare extended her hoof, and the Doctor shook it. "I'm in charge of the moon here, and princess of the Night."

"Hello, there, your majesty. I'm the Doctor, erm, Time Lord."

"Time Lord? You do mean Time Pony, right? The Time Lords do not associate with us Equestrians, but there are instances where the Time Lords regenerate into an equine form. We call them Time Ponies, just so the public does not freak."

"Oh...well, that's what happened with me. I'm the Doctor, Time Pony," he corrected.

Princess Luna scowled. "My sister and I do not particularly like Time Ponies. They have caused us hay before."

The Doctor's hopes sank. If the princesses didn't like him, he doubted anypony else would. "Erm, have there been Time Ponies before?"

"Oh, yes. Why, the first one was a fellow called Rassilon. he kept on trying to convince us he was some kind of ruler." She scoffed. "Not in my country.

Then there was some other mare or something, Susan. She had a strange name for Time Pony."

The Doctor hung his head. Susan was his granddaughter. "Anypony else?"

She shook her head. "I don't know this fellow's name, but I think he still lives someplace here. Manehattan or Trottingham, probably. Not sure. The point is, whenever they came, they always caused havoc. Rassilon destroyed the lost city of Marelantis. Susan got herself killed battling an evil pony that she brought."

A strange rumbling noise shook the town of Ponyville.

"Well, that's strange," Rainbow Dash said, looking out the window. "There aren't any scheduled storms today."

Princess Luna nodded to Derpy, who seemed like she was zoned out. "Let me go check it out. Come on, Doctor. Time to see if you're worth it."

~~~~~~

Outside, it was worse than anypony ever imagined. Across the sky was a lightning bolt, which seemed to be frozen on the sky, painted in electricity.

"That's new," the princess mumbled.

The Doctor flipped out his sonic screwdriver, scanning the area. "The readings are off the charts. Something about...alien technology."

"What? How? It's only a lightning bolt," Derpy said, who had suddenly appeared next to the princess.

"Yes, but what's keeping it frozen up there?"

The Doctor paused for a second, then spun around, and started running to his TARDIS.

"Where are you going?" Luna shouted to him, then, with Derpy, started running next to him.

"To my ship!" He replied.

"The blue box?" Derpy yelled to him.

"Yes!"

The TARDIS was standing at the same place it was a few hours ago, the lightning apparently unaffecting the blue police box.

The Doctor lifted his hoof, starting to snap his fingers. Then he remembered he had no fingers, so he removed the keys from his pocket, and unlocked the doors.

He entered the TARDIS, and opened the door so the princess and Derpy could get through. He liked having the company of a royal.

Sitting at the console, he pulled out a machine that had been hidden for centuries.

"What's that?" Luna asked.

"It's a machine. That goes ding." The machine "ding"-ed. "Ding."

"Okay."

Suddenly a crashing noise sounded through the TARDIS, followed by whispers.

Luna stood tall. "Who is it? I am Princess Luna of Equestria, and I demand to know."

A pink pony hoisted herself up from behind a bunch of crates.

"Pinkie Pie?"

The pony had bailed as soon as the Doctor started talking with Luna. Then a purple foal followed her.

"Dinky Hooves!" Derpy scolded. "How did you get in here?"

"It was unlocked."

The Doctor sighed. "Great. Okay, as long as we're all here, you stay in the TARDIS. I'll be right back, and I'll scan the lightning."

"Oh, no, you don't," Luna replied. "I'm going out there with you. This is my country, and I'll be the one to help you, thanks." She turned to the other ponies. "Don't you dare follow."

~~~~~~

Meanwhile, Twilight Sparkle and hundreds of other ponies gathered in the main hall. It was time for Princess Luna's speech for Night Mare Night.

Rarity had prepared all the decor, and Fluttershy got the music. It was all going to be perfect.

"And now, we introduce our beloved Princess Luna!"

Rarity pulled the curtain, and it moved on her will. But where the Princess was supposed to be, there was nothing.

"The princess, she's gone!" Rarity said.

Twilight gasped, and her eyes rolled back in her head. Then she fainted.

~~~~~~

Outside, the lightning was gone.

"What?" Luna gasped. "It's gone!"

"Yeah, I can see that." The Doctor took out his machine. It didn't go "ding".

"No alien life forms here."

Suddenly, the machine went crazy.

Ding! Ding! Ding! Ding! Ding! Ding! Ding!

"Oh. What do we have here?" the Doctor mumbled, and Luna stared at the sky.

"Doctor?"

"I'm busy, Princess."

"Doctor."

"Not now, Princess."

"Doctor!"

"What?!"

"Look up."

The Doctor did as he was told, looking up at the night sky. He stepped back, unable to breath.

"What is that, Doctor?" Luna asked, her eyes trained to the sky.

"That's impossible. What would they want with Equestria?" He mumbled to himself.

"Doctor! What! Is! It?!"

"It's a Dalek fleet."

Apparently, Princess Luna knew about the Daleks, because she stepped back, gasping. "No." Then she pointed to a dot next to the ships. "But what's that?"

The Doctor's eyes squinted, trying to catch a glimpse of the dot.

"Well, then, Princess Luna. Lovely to see you again." A deep voice said.

She gasped. "Discord?"

"Yes, my dear. But this time, I'm not alone."

He appeared in front of them, a mish-mash of animal bodies. Then a pegasus materialized next to him, the "Discord" creature, that looked strangely like somebody the Doctor knew...

"Hello, Doctor," the master said, flying a bit next to Discord. "Time to go bye-bye now."

The last thing the Doctor remembered was a grinning pegasus face as he fell to the ground, unconscious.