Doctor Whooves: Magic Through Time and Space

by The Doctor's Companion

Rating: teen
Tags: Princess Celestia, My Little Pony: Friendship is Magic, Alternate Universe, Doctor Whooves, Romance, Comedy, Adventure, Crossover, Twilight Sparkle
Length: 2926

The Advetures of Twilight and the Doctor

My name is Twilight Sparkle. When I was a little filly studying under Princess Celestia in Canterlot, I met a strange pony with a Blue Box. His name was the Doctor. He looks like a normal Earth stallion, but he's a Time Lord. His box is called the TARDIS, and it can go anywhere in time and space. When I grew up, he came back for me. I ran away with him, and we've been running ever since...

((NOTE: A basic understanding of the British television show, "Doctor Who", as well as bit of knowledge of the show "Torchwood", is helpful for full enjoyment)).

Credit for Cover goes to ~TheTitan99 on deviantART

Published 2012-02-04 19:45:36 UTC
Last updated 2012-03-18 19:33:17 UTC

Prolouge: The Filly Who Waited

Note: This is a sort of prequel to my other story, My Little Pony: Generations are Magic. Please, read that one as well and tell me what you think, as well as leaving suggestions for improvement. Don't be excessively cruel, though...

Prolouge: The Filly Who Waited

Canterlot Castle, Late at night

In the gardens of the palace, home to the sovereign ruler of all Equestria, Princess Celestia, all was quiet. Not even the screeching spider-monkeys made a single noise.

However, not all in this Castle were at ease. By the dim light of both her minute horn and a lit lantern, a small lavender filly, clothed in slippers and a pale blue bathrobe, nervously trotted the path of the foreboding gardens. Well, they weren't actually very foreboding, but the unicorn was still just a young pony, and the only reason she was out here instead of soundly sleeping in her bed was because she had heard a peculiar noise out there, and went to investigate it.

Sadly, she hadn't counted on how terrifying the path of the courtyard was in the dead of night.

"I know I heard something... but where-?"

Whiirr-rrr. Whiiir-rr.

A squeak escaped past the filly's lips, nearly causing her to drop her lantern. "There it is again!"

It was close by, she noted, seeming to come from behind a nearby bush. Cautiously, she walked over towards where the sound, which had gradually quieted until it ceased, peeking out ever so slowly to find-

A big, blue box.

"What the- Was... Was that here this morning?"

Upon further inspection, the filly noted that the box was something she recognized from a book she'd read over at the library. Back in the days when pony-skirts, mane-gel and Elvis Presfilly were popular, they'd had a communcation booth of sorts in Trotland, a Police box, which this seemed to be. However, those were really outdated, so why was there one in Canterlot gardens?

"I'd better ask the Princess about this..." The filly mumbled to herself, turning around. She didn't get two steps before running straight into somepony, though.

"Ah, hello, there! You wouldn't happen to know where the Princess is, would you? Oh, and some food, I'm starving. But not pears. I HATE pears."

The filly stared at this strange pony. He was a lot bigger than her, probably an adult at the least, definitely from Trotland, and had a coat that was this grayish amber color, his mane a much darker shade of that hue. His eyes were a color somewhere between gray and azure, and his Cutie Mark was of an hourglass.

"Uh..."

The strange stallion smiled, probably trying to be reassuring. "You know...? Princess Celestia? Ruler of Equestria? Raises sun and moon? Alicorn? Tall, white, tri-colored mane, is any of this ringing a bell? I really need to find her as soons as possible, so...?"

Suddenly, a thought came to the filly's mind. This guy... he might want to hurt the Princess! Maybe he's one of those "New Lunar Order" people who want to take down the Princess and bring the Mare in the Moon back from her prison!

The filly glared at him. "No way, Lunar Spy! I won't let you hurt the Princess!"

The weird pony blinked in utter confusion. "Pardon- OOF!"

Using an unusually large amount of magic for such a small pony, the young filly had made a sort of magical rope around the stallion's legs, turned him upside down, and then rammed him into a nearby tree. Repeatedly.

"Would- gah- you please- oof!- QUIT DOING THAT!"

"Twilight?"

Hearing her mentor's voice, the little filly dropped her captive and galloped over to the ruler, who currently had on a flowing bathrobe and fuzzy bunny slippers, as well as a look of complete confusion.

"Princess! Thank goodness you're here! I found this weirdo running around the garden and he asked where you were and then he said he hated pears and I think he's a spy and- HEY!"

Currently, the strange pony (who now had leaves strewn throughout his mane) had Twilight by the sash of her bathrobe.

"Tia, don't be alarmed, but this definitely is not a filly! She's obviously some sort of monster that was sent here to assassinate you! Do not be fooled by her cuteness!"

"The hay?! Why would I-"

At that moment, both were interrupted by a sound which neither of them had ever heard before.

The sound of Princess Celestia, raiser of the sun and moon, ruler of all of Equestria, professional prankster, completely and totally cracking up, tears streaming down her face.

"Dear Her I think she's lost it."

After a few minutes, the leader regain her composure. "Oh, I apologize for that, but you two are just too much! Let me introduce you two. Twilight Sparkle, I'd like you to meet my dear and longtime friend, the Doctor."

Twilight looked at her mentor. "Doctor? Doctor who?"

"Just the Doctor, Midnight Twinkle."

"It's-"

"Doctor, this is my most faithful and beloved student, Twilight Sparkle. She's got quite the talent for magic, doesn't she?"

The Doctor blinked. "So... not an assassin?"

"No more than you are. Unless there's something you're not telling me, Doctor."

Later...

"So, yeah, that's the long and short of it. I'm afraid that there's been no change in..." The Doctor took a quick glance at Twilight, who had been listening intently since the conversation began, "You-know-who's condition since the last time we spoke, Tia. I'm so sorry."

Celestia sighed, extremely disappointed. "It's not your fault, Doctor. I had hoped... they'd get better with time, but..."

The Doctor smiled sympathetically at her, then stood. "Well, I'd best be getting the show on the road. I've got people to go and places to meet!"

"Ah, Doctor, wait!" Twilight yelled, quickly running to catch up with the Time Lord, as she'd learnt he was called. "Is all that stuff true? The time travel, I mean?"

"True as the sun will rise!"

"And- And do you really save a lot of ponies's lives?"

"Ponies, griffins, dragons, not picky, really."

"Do you really go to other planets?"

"Of course! I just found a new one next Tuesday!"

"Can I come with you?!"

The Doctor turned and stared at her, startled by her question. "What?!"

"Can I come with you, please?! Your adventures sound so interesting! I want to see new things like you do all the time!" Twilight looked at him with the most innocent, adorable face she could make.
The Doctor swallowed nervously. "U-Uhh... Um... Tia? A little help?"
Celestia grinned wickedly. "I don't see a reason she can't go with on a short trip. It'd be educational for her." Plus she might actually have fun for once...

The Doctor glared at her, then turned his attention back to the filly. "Well... pack a suitcase, alright? Let me get the TARDIS warmed up and we'll be gone in about five minutes."

The filly grinned and started bouncing up and down. "YesyesyesyesyesyesyesyesYES!"

"Does she do that alot?"

"You have no idea..."

A few minutes later...

"Alright then! A quick spin to the future should get her up and running! Allon-SY!"

Whiir-rr. Whiiiiiir-rr.

As the TARDIS disappeared from the garden, Twilight came out, dragging a suitcase. And so she sat and waited for him to come back for her.

She waited all night, and he didn't return.

Twelve years later...

Whirr-rr. Whiirr-rr.

The door of the TARDIS flung open. "Okay I'm back, are you ready to- What the Discord?! Where are we?!"

Instead of in the Canterlot gardens, The TARDIS had effectively parked itself outside what looked to be a building made completely out of a tree.

"Great. Now I have to go figure out when and where I am so I can get back to that filly." With that, the Doctor walked inside the Tree-house.

Inside

"Can I help you?" A small, purple baby dragon asked.

"Ah, yes, could you tell me where and when I am? Got a bit turned around, I'm afraid, and I've really got to get back to someone."

The baby dragon blinked. "Wha... when you-"

"Spike, is someone at the... the... oh... OH MY LUNA!"

"Hello, there, miss, I'm- OW!"

Before he could introduce himself, the unicorn mare had magically thrown a book at him. A very large and heavy book for that matter.

The Doctor groaned, sitting back up after being knocked over. "What was that for?!"

The mare ran down the stairs. "It's you!"

"You threw a book at me!"

"You surprised me!"

"Why would you throw a book at somepony?!"

"Why did you say five minutes?!"

The Doctor blinked. "Wha... Twilight?!"

The Invasion of Ponyville, Part 1

Spike was having one odd, confusing day. First, upon waking up this morning, he had found Twilight sound asleep in the middle of the library surrounded by dozens of books, with parchment scattered all over the floor and a pen laying in front of her. This itself was not actually odd, Twilight usually fell asleep studying at least once a week, but what was odd was that instead of the typical historical fact books and magic spell journals, the books she was surrounded by had titles like "The Blue Box: Who is 'The Doctor'?" and "The Doctor: Real or Pony Tale?". When he'd asked her about the books, she stared off into space, then announced she needed to make breakfast, leaving his question unanswered. Unfortunately, while making breakfast Twilight had still been distracted by something, and thus was not paying attention to the stove.

After the fire department left (and Spike placed an order for new curtains), they'd decided to go out for breakfast. Even then, Twilight had seemed out of it. When the waiter had asked for her order, she'd stared at him for about two minutes before stating that she wasn't hungry.

And now there was this. A strange earth pony Spike didn't know had walked in and asked when and where he was, which was confusing to Spike because he didn't think it was possible to be any-when other than the present, and as he was about to voice that concern Twilight had walked in, freaked out, and thrown her copy of "Magic through the Ages: A complete Memoir of Starswirl the Bearded's Wife, Circe the Witch" at him.

Currently, the pair was staring at each other, the earth pony looking a bit sheepish, and the unicorn looking kinda ticked off.

"Soo... You live in a library."

"You're late."

"Er, right... Sorry 'bout that, can't always control the TARDIS. When did you get a baby dragon, by the way? Never saw him before-"

"I waited for you for twelve. Years. Twelve years! I went through four different and equally pretentious psychiatrists!"

The brown pony blinked. "Why four?"

Twilight looked away a bit sheepishly. "I... kept biting them. They said you weren't real, that I saw you because overwhelming magic."

Spike giggled. He vaguely remembered that. It was actually pretty funny to see them freak out when she sunk her teeth into 'em.

"What about the Princess? She knows me, why wouldn't she-"

"My mentor denied that you existed! When we were alone, she told me that the public couldn't know about the existence of time travel, so for the sake of keeping the peace, I had to go along with it."

"Oh, yeah. Forgot that she wanted that kept under wraps. I do wonder how she explains all the weird stuff that-"

Twilight stood, glaring at him. "DON'T YOU GET IT?! I SPENT THE LARGER HALF OF MY LIFE WAITING FOR SOME GUY THAT EVERYPONY TOLD ME DIDN'T EXIST! NOW YOU'RE HERE TRYING TO MAKE JOKES?! WHO DO YOU THINK YOU ARE?!"

"I... I-I think I'm the Doctor, and I'm very sorry that you went through all that, but I'm afraid there's nothing to be done about it at this point. Now that it's a fixed point in time, there's no way to change-"

"I DON'T BUCKING CARE ABOUT THAT! All I asked of you was that I might come along with you, and you left me waiting in the garden!" The lavender mare turned away and began to head back up the staircase. "You know what, Doctor? Forget it. Just... just leave."

The Doctor stared at her, a look of pained guilt on his face. "Twilight, I-"

"I don't want any excuses. All I ever wanted was to go along with you... but now... now I only want you gone. Get the hell out of my house." With that, Twilight retreated up the stairs.

--------------- Meanwhile, in an abadoned building outside of Ponyville------------

The old factory had become dilapidated over the years. The building had once been the largest producer of wickets in all Equestria, way back in the 50's when ponies had poodle skirts and Elvis Presfilly was just emerging as 'The King'. However, it was abandoned when the company went bankrupt from ponies realising that wickets didn't serve a lot of useful purposes. The only thing left in this place were rats.

At least, until today. For today, it had become the home base of a certain race of Time-Lord hating creatures.

"IT SEEMS AS THOUGH THE DOCTOR HAS PAUSED IN THIS SMALL TOWN OF PONIES. HE SHALL NOT LEAVE IT ALIVE."

"INDEED. FINALLY, THE DOCTOR SHALL BE BE EXTERMINATED."

-----Now back to the plot (literary, perverts!)----

The Time Lord sighed. Yet again without meaning to, he had ruined somepony's life.

How many did this make now?

Rosey... she was in an alternate universe... she couldn't go home...

Maretha... She'd been so in love with him, yet he cared too much about losing Rosey to notice...

Derpy... Nopony would ever take her seriously again...

While it was true that most of them had gone on to be happy, whenever he left them behind, their lives looked to be in shambles, and it was always his fault, his actions that led to it...

And now Twilight. All she had wanted was to come along with him, but he couldn't even do that. What's worse, he'd ruined it because of what he didn't do, not what he did.

Walking through Ponyville, he knew, was rather dangerous, due to the chance he may run into Derpy, but at that moment, a walk would do him more good than bad.

"Hi there!" A high-pitched, excited voice shouted in his ear, causing him to cry out in surprise and nearly fall over.

"GAH!"

"I've never seen you around here before! What's your name, where are you from, do you wanna be friends?!" The pink mare, to whom that voice belonged to, fired off in quick succession.

The Doctor hesistated for a moment, then answered the odd gum-colored pony. "Erm... I'm the Doctor, I'm from... Trottingham, and... I suppose it couldn't hurt."

The pink one bounced and giggled joyfully. "Yay! That's so great, Doctor... uh, what's your last name?"

"It's just 'The Doctor'."

"Okey-dokey, Loki! Well, come on, then, Doctor! There's lots to- Ooh! Lookie, there's more new ponies! They're kinda funny looking, though... Oh well!" And as quickly as she came, the pink pony was gone.

"... What just happened?"

Before the Doctor could ponder this further, however, a collection of shrieks burst from the village square.

"AAAAAAAAH! Wh-What are those... th-those... those monsters?!"

At that, the Time-Lord's head snapped up. "That would be my cue, I suppose!"

Galloping as fast as his legs could take him, the Doctor sped to the village's center, where a mob of ponies were huddled together in fear. Except for the pink pony who he had met moments ago, who was smiling pleasantly at the... the...

"Oh, bugger." The Doctor whispered in despondency.

"Hi there! Welcome to Ponyville!"

"IDENTIFY YOURSELF, PONY."

"I'm Pinkie Pie! Who're you?"

"WE ARE THE SUPERIOR BEINGS. OBEY OR BE EXTERMINATED."

"'Exterminated'? Like bugs? But that's silly! I'm not a bug! So, instead of that, how about we be friends?"

"DALEKS HAVE NO CONCEPT OF FRIENDSHIP." The robotic being turned to the crowd of terrified ponies. "WHICH OF YOU IS THE LEAST IMPORTANT?"

An orange pony with a Stetson and a blond mane spoke up. "An' just what in tarnation is that s'posed tah mean?!" She shouted angrily.

The beast didn't falter. "WHICH OF YOU IS LEAST IMPORTANT?!"

Another pony, this time a white unicorn mare with a stylishly curled purple mane, spoke. "Now you see here, you dirty metal monstrosity! We don't work like that here! All of us are important, no one less than anyone else!"

The herd of robots trained their laser-y bits onto the herd of equines. "IDENTIFY THE LEAST IMPORTANT OR BE EXTERMINATED IMMEDIATELY!!!"

That was enough. The Time Lord picked up a nearby stone and launched at the head Dalek.

"OI!" He beckoned them. As expected, the group turned to him. "I believe that I'm the one you lot are searching for, not them!"

"IT IS THE DOCTOR!"

"Yeah, duh!"

They trained their lasers onto the Doctor at that point. "THE DOCTOR WILL BE EXTERMINATED!"

The brown pony grinned mischeviously. "You'll have to catch me first!"

TO BE CONTINUED

For Clarification:

Rosey = Rose

Maretha = Martha

And now head-canon time! In my head canon, Derpy was basically the pony Doctor's version of Donna. She traveled with him, was awesome, etc., and then when the Doctor wiped her memory, he also messed up her eyes. She later married Pokey Pierce, who had Sparkler from a previous marriage. Dinky was born later.

Conclude Headcanon for Derpy Hooves!