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!