Operations

by IronPuddinG

Rating: teen
Tags: Twilight Sparkle, Gore, My Little Pony: Friendship is Magic, Dark, Human, Doctor Whooves, Adventure, Crossover
Length: 3403

What happens when the universe's greatest hero encounters the tall, faceless one of Equestria's past?

After the heartbreaking removal of Rory and Amy from his life, the Doctor decides to go into exile. But, as always, the Universe has other plans for him. During his voyage to his vacation spot, something goes wrong, landing him on the lowly planet of Equestria. The natives are peaceful enough; perhaps he can relax here instead?
Nope.
[Author's Note: I twist the ending of 'The Angels take Manhattan' a bit. I changed it to suit my head-canon, so somewhat of an alternate universe fic. Not enough to be labeled as such, however. Comments and criticism are appreciated.]

Published 2013-01-29 15:00:01 UTC
Last updated 2013-01-29 15:00:01 UTC

One

The Doctor sat at the park bench simply staring at the page he held in his hand. He read it over and over again to the point that he had memorized every word. The one page he had left. The last page.

Amelia Pond was gone. He would never see her again. He removed the glasses he wore on his face as he absorbed the words. There was one request on the page.
'There's a little girl waiting in a garden. She's going to wait a long while, so she's going to need a lot of hope. Go to her; tell her a story. Tell her that if she's patient, the days are coming that she'll never forget. Tell her she'll go to sea and fight pirates. She'll fall in love with a man who'd wait two thousand years to keep her safe. Tell her she'll give hope to the greatest painter who ever lived, and save a whale in outer space. Tell her that this is the Story of Amelia Pond... and this is how it ends....

"Oh, Amy, if only I could..." The Doctor quietly spoke to himself.

He couldn't return to Amy on that night when he crashed into her garden. He already had. One can only say goodbye so many times.

His thoughts drifted back to the graveyard. He sat there replaying the scene over and over again for another twenty minutes before getting up. He gently folded the paper and put it in his coat, careful not to bend it on it's way into his inner pocket. Then, he walked back to his TARDIS. He did not go to it with the familiar skip. He trudged, almost dragging his feet with his hands in his pockets.

That beautiful blue box of his was just ahead. He gave it a weak smile as he looked at his feet while he walked. Among the things he pondered on sitting on that bench was what was to be done. He would go into exile, never having any other adventures. The Universe didn't need saving anymore. He had done enough. He put the key in the lock and turned, opening the TARDIS. He stepped inside and went over to the controls. London, 1892, quite a lovely place during Christmas time. He stepped over to the monitor hanging off of the central spire. He pulled the keyboard from the bottom of the screen and typed in the destination.

The Doctor began flipping switches and spinning knobs seemingly at random. Yet, it was simply the work of a very experienced traveler with very experienced hands. The familiar hum sounded throughout the large room as the TARDIS faded from this destination into the directed one. But something was off... The Doctor couldn't place his finger on it but something wasn't as it seemed. Did he press the wrong button? No, he couldn't have, he was not clumsy. The speed of that thing in the middle of the spire, whatever it was?

His instincts were proven correct when the TARDIS made an unfamiliar sound followed by tremendous shaking. No, something definitely wasn't right. A buzzer began sounding relentlessly and the Doctor was suddenly flung from his controls as the artificial gravity in the time machine began to fluctuate from wall to wall. He had barely managed to right himself when the TARDIS shook again, triggering another fluctuation in the gravity. He grasped the nearest object, which happened to by a small table which was not screwed down. He was shot across the room as the lights blinked and the controls sparked, the artificial gravity refusing to remain constant. He flew from one side of the room towards the railing surrounding the spire. He stuck his hands forward in an attempt to protect his head. Fate, as it seemed, had other plans, as the TARDIS was rocked again by another tremor.

He lost focus of his surroundings and felt a tremendous pain in his head followed by a wave of sleepiness. He grabbed it in a futile attempt to remedy the throbbing that pounded in it. He was knocked across the room again, in which he landed on the opposite wall, sending another wave of drowsiness through him. He couldn't hold on much longer. He needed to stop this before he was eventually knocked out. As in answer to his thoughts, the artificial gravity stabilized for a few seconds, long enough for the Doctor to get up and hobble to the controls. There was nothing but a constantly shifting blur when he looked at them. He attempted to grab at one of the controls, but as soon as the stability arrived, it was gone. The gravity fluctuated and the TARDIS rocked violently as he was once again flung from his command module. The blow he received caused him to be knocked unconscious immediately, leaving the TARDIS free to take them wherever they were headed....

Ԅ

Twilight Sparkle sat in front of the fireplace in her hollowed out library home. Tonight was a very important night. Today was the first Friday of the year, the day to reread all the books in the library. It was a weekend, but it was something she enjoyed to do, and it was her responsibility to have a clear understanding of the material she would be borrowing out. After all, what good is a librarian who doesn't know what's inside the books that she was commissioned to look after? Twilight's horn glowed has it's magical aura enveloped the first book on the stack that she had gathered.

"Daring Do and the Curse of the Lost Tomb.", Twilight read aloud. Perhaps she had chosen the Daring Do series first on purpose, perhaps not. They had to be read anyway, so why not read the most interesting one first?

Twilight used her hoof to open the front cover, opting not to use her magic. Even though it was convenient, magic did not allow her the same joy as physically touching it. Magic could not feel. Without hesitation, she dove into the book, shutting out any outside distractions....

Ԅ

Some hours had passed and Twilight began to feel hungry. She looked up from her book and fixated her eyes on the clock mounted above the fireplace.

"Hmm, only eight o'clock," she said to herself.

She stood up and stretched her stiff frame, first arching her spine toward the ground, and then toward the ceiling, a satisfying pop sounding with each action. She turned around and walked into the kitchen. Upon arriving at the food-dedicated room, she went to the fridge, opened it, and scanned it's contents.

"Maybe just a light Daffodil salad," she spoke to nopony in particular.
Twilight began gathering the ingredients, making a note on her mental checklist about each one. She then opened a cupboard and levitated out a small salad bowl. She began to mix the ingredients.
Lettuce... tomatoes... Daffodils... croutons... she thought to herself.

Upon completing the meal, Twilight levitated the bowl over to the dining room table and sat down. On her trip over, she opened a drawer and pulled out a fork. She set the bowl and fork down at the table and then sat down herself. She grabbed the fork with her magic and jabbed it into the salad, stabbing a few pieces of everything. She brought the fork to her mouth and was about to bite down when she heard a boom from outside, followed by a low rumble.

Twilight let out an exasperated sigh.

"Vinyl had to pick tonight of all nights to have a party..." Twilight said with an annoyed tone. She bit on to her still levitated fork and pulled the salad from it with her teeth. The rumble was getting louder.

"It's alright, Twilight, it's Friday night. You should expect something like this." Twilight reassured herself.
She began working on the salad more, giving it more focus than she would normally. The rumble was still getting louder, so loud at this point that it felt like it was coming from right outside her window.

Then, a loud bang resounded just outside her window which was accompanied by a bright flash of light. Out of pure fear and instinct, Twilight dived under the table quickly, causing the salad and the bowl to fall onto the floor, the latter of the two shattering.
"Uggh, great, I'll have to clean that up later." She carefully got out from under the table and stepped around the large shards of glass so as to not break them into smaller pieces under her hooves. She trotted to the door and opened it with her magic. The sight caused Twilight to gasp in shock.

What sat in front of her was a large blue box which lay on, what appeared to be, its side. The impact had created a small crater surrounded by hot flames.

Twilight stood there for a few more minutes when she heard a voice, masculine, come from the box.
"Oi! Is anyone out there? If so, could you possibly open the door? It's a bit difficult from all the way down here..."
Did the box just talk? Did it come from inside? What did the voice mean 'all the way down here'? Is it alien? Is it friendly? Why did it have such a strange accen-

"Anyone? Anyone at all?" Twilight's thoughts were interrupted by the voice again.

"Umm..." Twilight began, "My name is Tw-"

"Ah! Good, there is someone," the voice called out again. "Listen, there'll be plenty of time for that later, but could you open the door please?"

"Oh, uh, of course! Just a second," Twilight replied. She walked rather quickly to the door, which was facing skyward. She enveloped the small nob in her magic and turned, causing the door to fall abruptly downward.

"Thank you very much," the voice said. "Now, I'd watch out if I were you."
Twilight quickly jumped back in response. A few seconds later, what appeared to be a grappling hook latched on to the side of the box. Why this voice would ever need a grappling hook to get out of a box no more than 4 feet wide was beyond her. After a few minutes of grunting, what looked like a claw grasped the side of the box. It wasn't an ordinary claw though. It had no talons and looked surprisingly soft. The creature within pulled itself out of the box. It hadn't looked like anything she had ever seen before. It was very tall, and it looked bipedal. It had long, lanky arms which had those odd claws attached to the end of them. It appeared to be wearing pants, overalls, a white shirt and a red bow tie. Twilight was at a loss of words for the creature who stood before her. The creature likewise looked just as confused as her.

"Were... you the one who opened the door?" the creature said first.

Twilight simply nodded and, in turn, the creature nodded as well.

"Well, thank you again. You have a name then, yes?"

"T-twilight. Twilight Sparkle," Twilight said shakily.

"Twilight Sparkle, eh? Well, I'm the Doctor, nice to meet you."

"You're a doctor?" Twilight said and began to scan him over once more. "You don't look like a doctor."

"Well, you see, I'm not really that kind of doctor, it's just the name, really."

"Oh... OK, then..."

The two stood there and looked at each other before the Doctor asked a question.

"Do you happen to have some rope?" The Doctor gestured slightly to his crashed vessel.

Twilight looked at the blue box and said, "I... don't think so. But, my friend, Applejack, has some."

"No, that won't be necessary. I was asking to save some time. Looks like I'll be going back down. Cherio!"

The Doctor then took the grappling hook back into the box.

Twilight called after him as she went up the strange box.

"Wait, Doctor! Down whe-"

She stopped when she peered into the box and stared down into the massive room contained in the small box.

"Go ahead!"

He snapped her out of her trance.

"What?"

"Say it!"

Twilight backed away from the entrance. She began to examine the outside of the box. She looked it up and down, even tried to look under it as best she could.

She went back to the entrance.

"It's bigger on the inside!"

"I just love it when people say that! OK, now it's not actually bigger on the inside it's more like another dimension."

"Another dimension? How is that even possible?!"

"Look, I would love to stay and chat, but I really need to run. I'll be pulling this thing up and heading off."

Leave? Now?

"What? You can't just crash in here and just leave like nothing happened!" Twilight said, putting some iron in her voice.

"Sure I can!" The Doctor called back. "And besides, what are you going to do about it? Use some silly magic or something?"

At that instant, Twilight's horn flared ablaze with purple energy. The Doctor was suddenly flung upward to eye level with the purple unicorn.

"Silly magic!?" Twilight practically screamed. "I'll have you know that I'm Princess Celestia's personal protege. I'm the most talented at magic in all of Equestria second ONLY to the Princesses. Now, unless you'd like to continue your puny life, I would suggest you show some respect!"

Twilight dropped the Doctor.

Why did I do that? The glare that she held on her face softened into a distant, concerned stare.

The Doctor got up, and pulled something out of his pocket. It looked like a pen, but when he popped it open, it's tip glowed and made a buzzing noise. He pointed it at her.

"Woah! I'm sorry, don't hurt me! I didn't mean it!" Twilight cowered under the metallic object. The Doctor said nothing as he pointed it up and checked it.

He pulled something out a wallet from his pocket and opened it. He showed her a blank page.

"Twilight?" he began, "what does this say?"

"It's blank. It doesn't say anything."

The Doctor seemed to be taken aback by this statement.

"Do you know what this is?" He asked.

"A piece of paper?" She responded.

"It's psychic paper. It supposed to say whatever I want it to say when I give it to you."

Now, it was Twilight's turn to look surprised.

"Somehow," the Doctor continued, "your mind resisted the effects of the paper...." He trailed off. He looked like he was trying to conjure up something.

"I need inside my TARDIS. Do you think you could level it out?"

"TARDIS? Is that what it's called?"

"Yes, TARDIS, Time And Relative Dimensions In Space. Now..." The Doctor trailed off and gestured slightly to his 'TARDIS'
"Oh, right, hold on," Twilight said. She closed her eyes and channeled all her energy into her horn, causing it to create a purple hue to envelope the small-but-not box.

After some grunting, the box slowly began to levitate. In the air, Twilight caused it to level out, and set it on the ground next to the crater. Twilight fell to her knees as she released the box.

With a small smirk, the Doctor said, "do you know how heavy that is?"

Twilight shook her head.

"It's over five million kilograms..."

The Doctor ran into his blue box and beckoned Twilight to come inside as well. Twilight, having regained some of her strength, stood up and walked slowly to the box. Before entering, however, something caught her eye. A glint of a shiny piece of metal laying on the ground.

She walked over to it and picked it up with a hoof. It was silver, but it was unlike any silver she had seen. it felt both smooth and rough at the same time. The most prominent feature, though, was the peculiar shape of the object. It was an empty circle with an X through it. It looked like somepony, or something, had carved out the hollow section. She had no saddlebag, so she opted to bring the silver piece into the TARDIS with her.

Upon entering the strange box, Twilight could see more than what she saw before. In the center of the large, dome-like room was what appeared to be a control station, which surrounded a large spire. The spire was hollow, and held a large metal piston which bobbed up and down in a steady motion.

"What is this thing supposed to do?" Twilight asked.

"Well," the Doctor started, "it's a time machine. And, it's a space ship. How 'bout that?"

"Don't be silly, time machines don't exist."

"A blue box with a strange being pops out of the sky and weighs over five million kilo's. Yet, it's impossible for a time machine to exist."

"Touché."

"Now, let's find out where I am..."

"You're in Equestria. This town here is Ponyville."

"PONYville! Isn't that clever. No, I need to figure out what time and where in the universe I am...."

The Doctor pulled down his navigation panel. He frowned at what he saw.

"Unknown? It can't be unknown, this thing has all the charts in the universe." The Doctor said. He banged his hand on the side of the screen. The image shook a little, but remained constant.

"There is only 2 reasons for that to not work. And it's not the first one," the Doctor turned to Twilight. "It seems we have a bit of a dilemma on our hands," the Doctor said. "Well, I guess, in this case, hooves." The Doctor chuckled a bit to his own joke. Twilight simply stood their, her brows knit together in confusion.

"Oh, they never laugh," the Doctor said as he turned back around. He began toward the stairwell connected to the catwalk around the control station.

"Wait! Doctor!" Twilight called after him. "Where are you going?!"

"Just going to grab something, be back in a jiff," he replied from upstairs.

Twilight sighed and began to look around a little more closely. She approached the control station and began to check all the knobs and buttons. It wasn't terribly interesting. She saw what looked like a picture sitting in between the edges of the station and the spire. It looked like another one of the Doctor's species. From it's features, it looked female. She had long, fiery red hair, wearing a white, horizontally striped shirt with a brown coat. Next to her stood another, male, with short brown hair. He wore a blue, sleeveless vest. They appeared to be standing here in the TARDIS when the photo was taken.

The Doctor soon returned with some ridiculous contraption attached to his back. From the top of the 'backpack', a metal pole extended above his head. At the end of the pole, stood a pair of green goggles, which was pressed against his eyes. Upon seeing what Twilight was looking at, he lifted the goggles.

"Ah, those are some old friends, Amy and Rory." The Doctor said. Twilight detected a hint of sadness in his words, but brought nothing up.

Twilight was still holding the silver piece in her hoof. It had apparently caught the Doctor's eye.

"Say, what's that?"

Twilight turned her head to face him, and then looked at the pendant.

"Oh, I found it on the ground outside just a few minutes ago."

"Hmm... have you seen it before? It certainly didn't come of this beauty."

"No, I only saw it tonight after you 'landed'."

"Interesting... can I have a look at it?"

Twilight nodded and outstretched her hoof towards him. He snatched it up and began to examine it. Almost instantly after he touched it, waves of visions and emotion surged through him, causing him to stumble back a touch. He took out his strange, pen-like tool and scanned the silver piece.

"Is something wrong?" Twilight asked.

The Doctor brought the tool to his face.

"Yes..." he began solemnly. "Something is very wrong..."

Author's Note

This is my first work that I've actually posted. Comments and criticism would be greatly appreciated. I'm also in need of a pre-reader. If you're interested, you can PM me.
Thanks for reading,
-IP
I'm also wondering whether or not I should have the Doctor Whooves character tag or not. I put it up there for now, but I can take it down if it's unnecessary.