AUTHOR'S OBLIGATORY DISCLAIMER: This is a work of derived fan fiction. I do not claim any ownership of any intellectual property related to "Doctor Who" or "My Little Pony: Friendship is Magic" which are the sole properties of their respective owners, nor do I intend to claim any profit from use of the trademarked and/or copyrighted characters from either of those works.
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CHAPTER ONE: An Unexpected House Call
Equestria: Day 1, Year 0 of Celestia's Reign
Celestia awoke slowly and grudgingly to a grinding noise inside her head. Her body and mind still ached from the previous night's final exertions, but they were nothing compared to the sullen soreness of her heart.
She'd done it. She'd banished her own baby sister to the Moon, Powers help her, she had done it and now, the morning after, she would have traded her favorite body parts to take it all back even though she knew it had to be done.
Her coat and mane were damp, and through the pounding in her skull she could hear the rumble of thunder and the hiss of heavy rainfall, coming through the holes that were blasted in the roof. Unwilling to open her eyes just yet, the alicorn mare stretched kinked muscles and stiff joints slowly, the grinding, wheezing static in her brain fading away with renewed blood flow.
That's when she realized that the sound wasn't in her head, but in the room with her. She opened her eyes, looking around the ruins of the throne room of the Palace of the Royal Pony Sisters in the Everfree Forest, taking in the holes blasted in the walls, stained glass windows blown outward by the sheer ferocity of the magic unleashed only hours before, and the hole in the roof, right where the moon had been in the night sky when Celestia used the Elements of Harmony to send Nightmare Moon - her Luna - to her prison.
She stopped as her eyes lit upon an incongruous sight. Sitting in the middle of the great hall was a blue wooden box, only large enough to fit one pony inside, perhaps two if they were feeling intimately cozy. Stenciled across the top and lit from within above the windows were the words, POLICE BOX, and a glass cylinder sat atop the entire contraption, blinking rhythmically then darkening as the noise the box made faded with a final THOOM.
She was still sitting on her haunches, staring wide-eyed, when the door opened and a chestnut earth pony with a wild shock of darker brown stepped out. His cutie mark was an hourglass, showing behind the blue pinstripe suit jacket he wore over a white shirt and red necktie. His odd appearance was complimented by the squarish spectacles on the end of his snout. "Blimey," he murmured, "Where did you bring me this time, old girl?" He glanced down and added, "And why am I on four feet?" Looking back at his flank, his eyes widened. "And why am I half-naked?" Turning around to get a better look, his gaze lit on Celestia and he stopped in mid-turn. "Oh! Hello! You're on four feet and totally naked, I supposed that's the custom around these parts, eh?" Tilting his head with a roguish grin, he added, "I suppose that's all very well, I mean, it wouldn't be the first time I've come across a culture like that although..." he drawled, "It's the first time I've been a four-legged... horsey... thing."
Celestia just blinked as he finally rambled to a stop, and murmured, "Who... what... how?" She was too stunned to even prime defensive spells into her horn as she watched the strange, strange pony continue examining himself.
"Let's see... that didn't feellike a regeneration, but I suppose there's a first time for everything." He started patting himself all over with his forehooves, muttering, "Head, got that, only one of them... tch... still not a ginger. Pity. Eyes, two of them, oddly forward-facing for this kind of body, hands... no hands, but circular, semi-flexible hooves? That's a new one!" He lowered his head to look under himself, tail switching back and forth. "Oh, a tail! I always wanted one of those! Let's see, hooves for the back feet, and oh thank god that's still there, don't want to be like the Corsair and gender-switch unexpectedly WELL!" He proclaimed, favoring the Princess with another roguish grin. "Now that I've made sure everything's where it's supposed to be, I'll answer your questions in the reverse order: What? Time Lord, although I suppose Time Pony might be more apropos. How? In this box here, it's my TARDIS, Time and Relative Dimensions in Space. It's how I get around the Universe. Who? That's the easy one! I'm The Doctor."
Celestia just blinked for a moment, trying to pull herself back together as she staggered to her hooves. "Doctor... who?"
"No, just the Doctor, although 'Doctor Hooves' might be a nice little pun, don't you think? Blimey," he murmured, peering at her over his glasses, "Are you all right, miss?"
Shaking her head, Celestia murmured, "I am about as far from 'all right' as it is possible to be and still be in Equestria, Doctor, but it's none of your concern."
Sniffing the air, the Doctor peered around. "Are you quite sure about that? Because I must say, me arriving here all ponified and you looking like you've just been through something totally horrible is a very large coincidence, and if there is one thing I absolutely do not believe in, it is any coincidence larger than a bread box." He stepped around her, circling the alicorn slowly. "Plus, this place positively reeks of artron energy! I haven't seen this much since the last time I tried to use the Eye of Harmony to make instant popcorn." He noted Celestia's shocked expression at the name and added, "I was really really hungry, and really REALLY bored. Never let a Time Lord get bored. No good can come of it." Nosing into the pocket of his jacket, he fished out a small cylinder with a blue gem on one and and muttering something about lack of proper fingers, managed to get it into the corner of his mouth, biting down on a switch in the middle. With each bite, the gem lit up and a buzzing sound like a thousand hyperactive cicadas emanated from the device. "This place is absolutely soaked in artron residue. That must be what pulled me off course, triggered a transformation if not a full-on regeneration. No telling if it's permanent or not." He tucked the rod away and turned to Celestia. "I say, what happened here? It looks as if there was something very violent." He trailed off as he saw tears start to trail down the alicorn's cheeks. "...What's the matter, miss?"
Barely holding back a sob, she lifted her gaze to meet his. "I am Princess Celestia, now the sole ruler of Equestria, Steward of the Sun, and now Regent of the Moon. As for what happened here... I did it. I didn't want to, but I did."
Stepping just a little closer, concern mixing with suspicion on his face, the Doctor murmured, "What, Celestia? What did you do?"
Celestia dropped to the floor, laying her head on her hooves. "...I took the Elements of Harmony, and sent my sister to the Moon, never to return."
The Doctor just looked at her for a long moment, then murmured, "I'm sorry. I'm so sorry." Catching the note in his voice, Celestia shook her head and replied, "She's not dead, Doctor. She's imprisoned, along with the monster that took her over from within... and I fear, more than anything else, that I will never see Luna again, not as anything other than Nightmare Moon."
"Celestia, I want you to look at me. I know we've only just met, but I want you to listen as well, and trust me when I say that will do everything I can to bring your sister back."
Confusion creasing her brow, the alicorn just stared at the madcolt with a box and asked, "Why? What can you do? I'm immortal, or as close as you can get to it, and so is she. Right now, I'm the most magically-endowed pony on the entire planet, and I probably couldn't bring her back if I tried, not without bringing Nightmare Moon along with her, and I doubt that she's going to change her mind anytime in the next few thousand years.." She narrowed her eyes, horn flaring to life as she studied him with senses both physical and magical, and what she saw made her eyes go stark wide, pupils shrinking to pinpoints. "Wh-what... Whatareyou?"
The smile completely gone from his face, the Time Lord replied, "You say that your sister's been taken by a monster, Celestia. I don't know if this 'Nightmare Moon' has ever heard of me, but she will. Most people run from monsters, or fight them. Sometimes if they can't do either of those, they join the monsters, well let me tell you something, my dear Princess; I'm the Doctor..."
"...and the monsters run from me."