Time, Space and Magic: A Doctor Whooves Journey

by weimaj

Rating: mature
Tags: Doctor Who, Gore, My Little Pony: Friendship is Magic, Death, Alternate Universe, Human, Doctor Whooves, Princess Luna, Original Character, Porn, Science Fiction, Suicide / Self Harm, Derpy Hooves, Violence, Crossover, Sex, Anthology
Length: 3190

What would happen if an impossible blue box fell out of the sky?

"This is the story of a mad stallion and his impossible magic box. It's a story of hope and hopelessness. Love and loss. Science and magic. This is the story of the Doctor and his search."

Features so many different ideas from years of writing, theorizing and planning. The tags are there for future chapters, which will include gore, death, self-harm, violence and a lot of gratuitous smut, which also means SHIPPING.

Oh, and yes, this is a crossover with Doctor Who, circa December 1st 2013, in terms of Who time, and begin primarily around the events of the 1000th Summer Sun Celebration. The italics in the story take place concurrently with the events elsewhere, but are not in the timespan previously mentioned.

The story will be told out of order, due to the erratic nature of time travel, hence the Anthology tag.

Published 2019-07-27 00:00:01 UTC
Last updated 2019-07-27 00:00:01 UTC

The Wedding That Only One Pony Would Forget

The big day had arrived. After a week of planning (helped by the use of the TARDIS), the alien-turned-pony was ready for his moment.

It had been a long few months for the Doctor. Ever since he ran into the horrible, grey version of himself, he'd lost so much. His happiness, his masculinity... his wall-eyed marefriend... He sighed at the mere thought of her. 'No, we agreed to never look back. Just like before...' An image of a young human girl flashed in his mind, her blonde hair highlighting her smile...

The Doctor shook his head. 'Focus.' He needed to. Today was a happy day. One he hadn't expected to be so soon, but why bother waiting? Waiting normally led to bad things, like invasions, or explosions, or magical interference from the enemies of the Princesses. 'Still haven't shaken off the feeling of being drained... timeline hopping is more dangerous now...'

The Time Pony moved around to the other side of his personal ship, checking the local environment, when a voice echoed from within a side-chamber.

“So, Doc... today's the day you get the perfect mare for you.”

Doc. He hated that abbreviation. At least it wasn't 'Prof'. The Doctor turned to the source of the voice.

“Is that a hint of jealousy in your voice, Mysti? Worried about her taking your place?”

The mare down the hall scoffed. “Jealous? Me? Never. I'm just worried you'll run off like the Archives said...”

“I told you to stay away from there!” He glared down the hallway, mentally reminding himself to talk to the living embodiment of his blue box about this. “You're getting too close to MY Tard-”

A giggle reverberated from within the depths. “YOUR Tardis? Doctor, you lost her to that other version of you a while ago, remember? Or are you getting forgetful in your old age~?”

The stallion played with his bow tie in frustration – or as much as he could without fingers. God he missed those. “Old... I'm still young. I'm probably younger than Celestia.”

The unicorn from the other room finally approached. She had a cute bonnet on that complemented her black mane, and a long dress she must've grabbed from within the extensive closet. Mystical Heart, a dangerous, secretive mare after the Doctor's heart... to what end, he hadn't figured out yet, but he'll get there. He always does.

The Doctor raised an eyebrow at her apparel. “I don't remember you getting an invite.”

“Aw, come on. Can't you let me come just this once? What could possibl-”

“Dalek invasions, changeling attacks, more mes, a crazed local baker on a friendship high... should I continue?”

The mare sighed and took off her hat. He was right, of course. He normally was. This time, however, it's almost like... “Are you worried about something happening, or are you hoping?”

It was his turn to sigh. “You've seen how bad my history with weddings is. Even the ones that aren't mine go badly. The only one that went anywhere near well happened in a dying timeline with a robot body.”

“Poor Melody. I'd have like to have met her.”

“I don't think I would.” He wanted to forget her too. He needed to, just for today. “You are needed here. If anything goes wrong... anything at all... you are to land the TARDIS in the church and I'll find you.”

Mysti nodded and used her limited magic to levitate a top hat onto his head. “Well then, give my best wishes to the bride.”

“I think we'll be a bit busy for that. But I'll try.”

She snorts. “Don't keep her up all night.”

The Doctor turns and leaves, making his way out to Ponyville, Equestria from his impossible mobile home.

The human sat up straight from his bed, laptop shifting from his stomach. Having been at school all day, he had needed to let his creative juices flow. The young man looked at the time, realising he was leaving soon. He had just enough time to pack his bags, when his ride – his father – showed up. What he didn't realise was the laptop cable laid on his bed as he walked out the door...

The Doctor stood at the giant wooden doors, nervously looking around. Nervous... funny, he'd never be this nervous again... but then again, he never expected to be getting married again, especially so soon. He slowly walked inside, as if expecting some monstrous creature to jump out at him, as had happened many a time in his long history.

The main hall was already starting to fill with a few familiar faces – some of whom he knew quite well – including one purple mare who bounced over excitedly. She'd been careful to hide her true identity to everyone else, but to the Doctor, she was instantly recognisable. After all, she was his daughter.

Moondust approached looking excited but also apprehensive. Her long mane was in a cute ponytail – what exactly did they call that hairstyle? - and was wearing a long gown to cover her wings, a far cry from her normal hoodie. “Papa, you made it on time!”

He smiled at her, thinking back to his last visit to the house of Faust. “The TARDIS wouldn't let me be late twice...”

The younger pony pouted, reminding him of her mother – another lost flame. “I still don't like you disappearing on me, especially to gallivant off with some floozies...”

He frowned at her, equally disapproving of her language choice. “I seem to remember you being the one who needed her own space with her husband...” He looked around, concerned. “Speaking of, where is he? I thought he'd be here...”

The mare looked away, disappointment oozing from her. “He was, but then he called away...” She looks up her father, still the scared little filly he'd raised.

He put a hoof up to her face, then around into a hug. He blamed himself for this reaction, since he was the one who repeatedly went away on “trips”, leaving her in the hands – er, hooves – of her aunt. While not ideal, she was at least caring... well, her servants were, at least.

She smiled at his touch, nuzzling into him gently. “So, are you ready? This is the most important day in your life...”

“No, that was when you were born, Moony.”

She blushed and turned away slightly. “Just answer the question, silly.”

“I'm as ready as I'll ever be. I just hope she's ready too.”

The doors opened and a white unicorn stepped in. Being the dramatic type, all eyes were immediately on her, but that was nothing new. The new member of the congregation searched for the sign of a bow tie, and landed on the usual suspect – the one with an equally formal hat.

Moony quickly pulled away. “I think she might need to speak to you.”

The Doctor nodded in agreement. “I'll see you after the wedding... hopefully.” Working his way over, he tried to read the mare's face: worry; sadness; confusion... he really should work on reading a pony's expressions. As he gets closer, his target speaks.

“Burgundy bow tie with a mauve hat?” Disgust. As expected, Ponyville's resident fashionista didn't quite understand his taste in clothes. “Doctor, darling, you should've come to me. I was trying to convince her to drag you to the Boutique for a tuxedo fitting...”

The Doctor flashed Rarity a toothy grin. “I'm not good at keeping appointments.”

She sighed. “And that's why your bride-to-be is late too. We had some last minute... changes to the dress and there was a distraction involving one of her furry friends.”

“Not unexpected, of course, but we'll manage. Is that all, because you still look worried and that's never a good thing for you.”

The mare closed her eyes and breathed slowly, trying to get her thoughts into order. “I haven't heard anything from Applejack. Nopony's seen hide nor hair from her since the Canterlot invasion. Nopony except... you. Why?”

The Doctor looked away. Applejack... his most recent regret. A one time fling that backfired... “I don't know. She was okay when I checked on you all, but... I don't know.” The Doctor did as he would always do. He lied. Ironically, given Applejack's role with Honesty.

The Generous Spirit before him huffed slightly, but didn't pressure him. He didn't need it, not on his wedding day. Plus she could always convince his bride to help her once this was all over anyway. “I'm also not sure about my other role today. Why me? Could you not have asked Twilight? Or maybe one of the Princesses? I'm sure they'd be happ-What are you grimacing about, Doctor?”

“My relationship with the Royal Family isn't the best.” He glanced over at a pony in the crowd, but looked away before Rarity could make out which one. Possibly that mare from before? But she's a unicorn, clearly... “Anyway, I figured since you're the one with the most upper-class accent in town, you should do it. Plus... you're one of our closest friends.”
That caused her to giggle a little bit. “I'm just a humble mare from a small town.”

“Humble? You?” He snorts slightly. “You're funny. Have you learnt your lines? Of course you have, you're... well, you.”

Unbeknownst to either pony, an orange mare had managed to sneak into the church. She looked broken, like a soulless husk in comparison to her usual, gung-ho self. Finding a quiet spot, she sat away from most other ponies in the church as it filled up, the hour drawing nearer and nearer.

A few hours had passed in the time since the human arrived at the closest place he could call home. He had expected to see his grandparents, but wasn't expecting them to be so okay with his recent obsession with technology. It was at this point he realised his conundrum, but there was nothing to be done. He opened up his laptop, changed it to power saving mode, and began to type...

The Doctor had taken his place by the altar, waiting increasingly nervously. The muttering of the stallions and mares behind him – most of them friendly with either him or his soon-to-be wife – certainly wasn't helping.

All of a sudden, the organ began playing. 'My old mate Jesus would probably be confused by this entire situation... poor bloke couldn't even handle keeping a magic trick with water quiet...' This thought relaxed him significantly, as the pegasus mare called Fluttershy arrived beside him.

The whole way to the church had been the single most scary thing Fluttershy had lived through... until she entered, anyway. And that's including facing a draconequuis bent on reigning anarchy over Equestria and dealing with a sleepy hundred foot dragon. But she made it. Even if her mother wasn't there, she could at least write to her about the wedding she dreamed of since she was a little filly, with a nice, kind, caring stallion by her side.

She smiled up at him, since she was a few inches shorter. He winked back, as Rarity began the proceedings. Rainbow Dash was hovering in anxiety, probably because she'd be the one to drag her best friend back if she ran. Twilight Sparkle, being the wedding planner, only half-listened, the reception plans weighing on her mind. Why Twilight and not Pinkie? Since Sugarcube Corner was still open, the Cakes needed her there. Thankfully it was also giving them enough time to make the wedding cake.

Applejack stood up and walked closer to the front, softly singing a song about unrequited love. Some of the congregation began to take notice, but Rarity – one of her closest friends – stood firm at the altar opposite the mysterious stallion and her other, just-as-close companion.

The Doctor, given the cue, turned to Fluttershy. A small white rabbit hopped carefully forward, carrying a pair of bracelets upon a silk cushion. Fluttershy picked one up, smiling down at her bunny friend in appreciation of him being there for her once again. The Doctor took the other, and with two simple words, she offered her hoof to him, allowing the stallion to slip the gold band on her. She then reciprocated, holding back tears from happiness.

Rarity then turned to the crowd to address them, becoming slowly aware of her farmpony friend's attendance. “If there is anyone who believes these two should not be married, speak now or forever hold their peace.”

Applejack stepped right up to the groom, tearfully but wordlessly demanding his attention. Fluttershy gawked at her, looking confused and worried. The freckled, blonde mare decided to ignore her unanswered question, instead simply asking the Doctor one question...

The young man had never been in a relationship before, so this situation was new to him. The question that this person had posed never crossed his mind. He'd witnessed the events happening to his (admittedly very limited amount of) friends, but this was an unexpected quandary. Go with the girl who he'd befriended and, truthfully, felt emotion for, or go with the complete stranger who was never supposed to be in the narrative to begin with. Silently wrestling with the predicament was causing him to run out of time and battery, so he left it to fate. A virtual coin flip on a website. With his next click, his life and the plans he made for the future would change...

Applejack walked away, crying and dejected. This impossible stallion who showed her another world and put her in immense danger, this creature who made her feel special in ways she had never felt before... had chosen her friend over her.

The Doctor turned back to Fluttershy, a small hint of sadness in his large, old eyes. He always was a heartbreaker – not even royalty could stand up to his charms, nor family members it seemed. He sighed softly, then did what he'd always do in any emotional moment: he smiled at the most important female in his life.

Rarity, while looking over at Applejack's retreating flank, said in a quick manner, “You may now kiss the bride.” Without waiting for the potentially voyeuristic show, she left to tend to her friend, to make sure she wasn't attempting to do something dangerous.

Applejack didn't know where she would go. Applebloom wouldn't understand, and if Big Mac found out about this, the Doctor would need a hospital... or even a morgue. No, as far as she was concerned, she had nothing left. She stared at a flickering candle and, without flinching, gave in to her instincts, the urge she always got when she felt angry, betrayed or hurt. She kicked.

Rarity ran back out to the packed hall in a panic. She received a lot of odd looks until she explained in one simple, all-encompassing word. “Fire!”

Chaos reigned. Discord would've been proud, had he not been busy acting as a bird toilet. The congregation stampeded out the hall one way, with one lone stallion running the other. He should've known. Something always – ALWAYS – happened, and this could be the one to alter the future. Running towards the source of the already large smoke cloud, the Doctor charged in. Standing there, emotionless, was Applejack. She looked at peace with the world, with no visible intention of moving.

The Doctor tried to put out the fire, but with the wooden structure around them, it wouldn't take long for them to suffocate. The crowd outside were audible, even from the other side of the church, but – there! The sound of an engine, wheezing as the brakes grind. The Doctor, having no way of dragging her into the increasingly solid blue box in the corner, put his hooves to her temples. He'd only been forced to telepathically link with one other mare in his time on this world, but this was an emergency, so there was no time for subtlety. With one mental command, the farmer passed out.

Mysti stood in the doorway of the TARDIS, and moved the now sleeping mare into the ship, while the Doctor got busy taking off. He wasn't in the mood for talking, but that didn't matter – the scanners had shown the whole thing. The unicorn felt bad for Applejack. It wasn't her fault she got mixed up with the two hearted stallion with an enormous sense of sentiment. Finally, she spoke.

“We have to wipe her memory of what happened. Make it look like an accident.”

The Doctor fiddled with some knobs on the console. Of course, he knew that. She'd be imprisoned for arson if she was found out. Not even her role as a holder of an Element of Harmony would prevent that. “I'll do it. You fly us to Sweet Apple Acres, just in the orchard.”

Mysti took his place at the central column. “I'll contact Rarity about keeping quiet. She seemed to be distracted by something even after you ran in to the fire.”

The Doctor ran a hoof through his hair. “What about Shy? Did she make it out safely?”

Mysti smiled over at him. “You're going to need to give her the best honeymoon ever after this. She nearly watched Angel get trampled under the rush.”

He grimaced. “I hope he's not as vengeful as Spike told me...” That dragon, while still just a baby, had a lot of tales about the animals and citizens of this town.

Mysti bowed her head slightly as the TARDIS lands. “You're going for a trip again aren't you? Alone, I mean.” Seeing his nod in response, she swallowed. “Was this always the plan? Or is this just convenient?”

“You know what I'm searching for. I need all the time I can get... especially given how uncertain this timeline is.” He needed to get back on that search soon. “In any case, I have a tonne of research to do. Plenty of places to explore.”

Mysti turned towards the door. “I'll let Fluttershy know, then.” Pausing just outside the machine's entryway, she looked back. “By the way, that's 20 you owe me.” Smiling slightly, she trotted away, heading for the distant town. The Doctor stood next to the unconscious Applejack, sighing. “I wished you'd let me wipe her memory so you could help move her, too, Mysti...”

Finally, the battery drained its last drop of energy, and the laptop fell asleep. The human was heartbroken. He'd hurt not only the first woman he could truly say he loved, but also his friends. He hadn't taken up the role of a character who crossed dimensions in hopes of getting a girlfriend, but now that his character, his Doctor, was married to the mare he called a waifu, he knew... she was his. It was going to be a long weekend, but for the first time in years, he couldn't wait for Sunday, when he could explain his sudden disappearance, and move on to phase two of his plan.