The Raggedy Doctor Hooves

by Flutterguy89

Rating: teen
Tags: Rainbow Dash, Doctor Whooves, Original Character, Fluttershy, Adventure, Crossover, My Little Pony: Friendship is Magic
Length: 9437

When they were fillies, Rainbow Dash and Fluttershy had an imaginary friend, but when they grew up, he came back.

An imaginary friend. That is what Fluttershy and Rainbow Dash had decided the mad pony in the box was, but the raggedy doctor was far more than that. When the supposed-imaginary Doctor appears in present day Ponyville, looking as though mere seconds has passed since they last saw him, Rainbow Dash and Fluttershy are in for some very real trouble.

((Heavily inspired by the Doctor Who episode "The Eleventh Hour," as such it will contain plenty of references but the story goes in its own direction. Conceived as an 'episode' with subsequent sequels acting as other episodes in a larger series.) )

Published 2013-04-23 21:30:01 UTC
Last updated 2013-06-02 23:27:00 UTC

Prologue

Prologue

An exhausted earth pony stallion trudged across the metallic floor, his hoof-falls echoing ominously in the domed chamber. The pony was struggling now. Each movement he made was becoming more and more taxing. He lifted a shaking hoof and pulled a lever on the central console, and the room lurched as TARDIS engaged its flight.

Sweat was beginning to pour off of the pony now. Despite all the time he had been through this, it still hurt. It always hurt. His vision flashed white and he collapsed to the floor, twitching with the torment that would save his life. Save his life. Well in a manner of speaking that was correct, but he would still be gone, nothing more than a memory of a life in another pony.

He pushed himself to his hooves, casting his gaze about the TARDIS, his TARDIS, for the final time. Tears began to moisten the corners of his eyes. He’d never them again… all his friends, his companions… not with these eyes. Before they could fall, his tears evaporated, rising in motes of golden light.

“I…I don’t want to go…”

Energy tore free of the stallion’s body, channeled through his face and fore-hooves. A powerful scream tore from his throat. There was fire. Explosions. Something was wrong. Columns fell. The TARDIS shook as it exited the time vortex, falling through space, hurtling back towards the Equestrian surface.

The energy subsided, and lying crumpled on the floor was the Last of Time Turners. His tan coat was now a dull slate, his spikey brown mane transformed into a flowing black.

“Oh… Oh blimey, who am I? What am I? Oh, this all so new!” The pony exclaimed as he examined his hooves, “Ooo lookie here, I’ve still got you my pretty little hooves. I love hooves, who doesn’t love hooves? Things with hands maybe… but hands? Ha! Who needs ‘em? I don’t!”

The pony pumped a hoof in the air triumphantly, oblivious to ruinous state of his vehicle.

“And look at this mane, I got hair for days! Oh I’ll need to buy more shampoo, there was always this one in Equestria that made just the right kind of bubbles. Maybe I can ditch the pomade though, sleek over spikey! New Doctor, new mane!”
An almighty explosion rocked the TARDIS as it streaked through the Equestrian sky like, falling like a blue meteorite. Suddenly there was a loud “Foomf!” sound. The TARDIS punched through a layer of the Cloudsdale residential district, leaving a distinct hole in the sturdy cloud’s surface. Whether the regeneration addled Doctor realized it or not, the cloud had slowed his decent just enough for the TARDIS to make an entirely ungraceful but definitely survivable crash-landing.

“First floor. Parking.” The Doctor said as he giggled to himself.

A lantern clicked on, throwing the walls of the little tent into sharp relief.

“Did you hear that, Flutters?” A voice drifted out of one of the two squishy sleeping bags. Specifically the one with the unruly tuft of rainbow colored mane sticking out of the top.

“Y-yeah…Wh-what do you think it was?” Replied the other sleeping bag, its voice quivering.

The head of a cyan filly popped forth from the first sleeping bag as the young pony moved into a sitting position. “We should check it out!” The little filly said excitedly.

“But what if it’s dangerous, Dashie?” The head of a buttery yellow filly with a flowing pink mane that partially obscured her face became visible as she mirrored her friend’s posture.

“Pfft, there’s nothing I can’t handle out there. Beside it’s, like, the perfect thing to do during a backyard campout. We can go explore, awesome right?” Rainbow was already hallway out of her sleeping bag now, wiggling a bit to free her flanks from the poofy confines.

“O-okay…” The yellow filly climbed out of her bag, having some difficulty extricating her too long legs, but by virtue of some natural grace she was able to climb out without as much trouble as her friend. The friend in question was failing to find any traction with her back hooves and with a grunt of effort flipped forward, performed an unintentional summersault, and rolled into the tent’s wall.

“Meant to do that...” The cyan filly grumbled, while her friend covered her mouth with a fore-hoof to politely to hide her smile.
Before long the pair emerged from their tent and made their way through the quite backyard. Rainbow Dash carried in her teeth the lantern from the tent, shining its light around the deserted landscape in order to check for monsters, wild beasts, or grown-ups. Fluttershy followed close behind her friend, more than once bumping into her flank when the cyan filly had stopped short.

During once such incident Fluttershy murmured a quiet “I’m sorry,” only to be shushed by her friend. Fluttershy shot her Rainbow a pleading look, but the filly only pointed ahead with an outstretched hoof. Fluttershy gasped, there ahead of her in the clouds was a hole. Not just a little hole that a foal would dig in the clouds for fun, but a real honest-to-Celestia hole that went straight through Clouldsdale.

“Oh…oh my,” the yellow filly managed as her companion too the opportunity to edge closer to the hole.

“There’s something down there, all the way down, on the ground,” Rainbow voice began to grow excited, the gleam of adventure shining in her eyes.

“Oh no… please Dashie, no…” Fluttershy began to plead, taking a reflexive step back.

“Oh come on, it’ll be fun, and I don’t want to go alone…” A sudden idea popped into her rainbow adorned head, “If you do this for me I’ll go see the next five migra-whatsit things you were going on about with you.”

Fluttershy gasped, her eyes going wide with excitement, “The butterfly migration! They… they only come around every few years… You’d do that?”

Rainbow Dash gave her friend a playful nudge. “Yup! And all you gotta do is come with me to check that thing out.”

The pair of fillies made their way down through the hole in the clouds, with Fluttershy resting on a miniature cloud chariot which was being expertly lowered by Dash. Fluttershy was still having trouble flying in thinner air of Cloudsdale, so the two friends had worked out this little system as a way they could visit Fluttershy’s animal friends on the surface. Except they usually did that during the day… and they usually told their parents where they were going.

Before long the object they were seeking came into view. It looked like a…blue box?

“Wh-what do you think it is?” Fluttershy asked timidly.

“I don’t know, but I’m gonna find out!” Dash said as she lowered her companion the final few hundred feet.

As the cloud touched down, Fluttershy extended a shaky foreleg and tested the grassy surface. She let out sigh of relief and began to smile, happy to be back on terra firma. The shy filly fluttered her wings and hopped off her little vehicle. Dash gave her friend a little smile, the cyan filly never quite understood Fluttershy’s love of the ground but the timid filly’s good mood was always contagious.

However their good mood was short lived. A sound like the tolling of a deep bell sounded from within the blue box. The fillies looked at exchanged looks. They approached the box together, and despite her earlier bluster, even Dash couldn’t help but shake a little.

The pair heard a hinge squeak, stopping them dead in their tracks. Suddenly a puff of smoke rose from the interior of the rectangular box and out popped the head of a grey stallion.

“Oh, hello there! Do you have an apple?”

Author's Note

I'd been thinking of writing this for a while now, and I'm really excited to share it! I was planning on waiting until I had a few more chapters in the hopper before posting this, but I just got too excited after finishing up the prologue.

So enjoy some fun Doctor Hooves action!

Chapter 1

Chapter 1

“An…a-apple?” Fluttershy managed despite her wide-eyed disbelief.

“Uh huh, an apple! All I’ve ever wanted my whole life is an apple!” The stallion climbed out of the box and lowered himself to the ground.

“Whoa! Did you, like, get some pegasi to fly you up into the sky in that thing and then drop it?” Rainbow was literally hopping up and down on the spot, her little wings buzzing with excitement.

The grey pony began to mirror the little cyan filly’s action, hopping with excitement. “No why? Would that be something I should have done?”

Dash abruptly stopped her bouncing and gave the pony a quizzical eye, “Uh… I just figured ‘cause your box fell… why are you jumping?”

“I thought this was how you ponies said hello, and that the little yellow filly was just being rude by not jumping too.” The earth pony stopped his bouncing and tilted his head. “Are there any rituals that I should be aware of? The moon ponies of the 37th century stick their tongues out and wink, should I do that? I just don’t know… oh and do you have any apples? I’m starving!”

Fluttershy approached the earth pony, “Um… saying ‘hello’ is okay, and we don’t have any food with us… but there is a little forest nearby, I’m sure we could find some berries…”

Rainbow gave her friend a nudge and a significant look, before whispering to her. “I don’t think this guy’s all there…” She twirled a hoof about her ear in the universal gesture for ‘craaaaaaaaazy’.

“I know…but maybe we can help? I mean… he doesn’t look so good.” The buttery filly whispered back. Then in sudden flash of inspiration she added, “Is going into the forest at night too… um… big of an adventure?” Her confidence broke about halfway through the statement. After all, she was manipulating a friend… but that poor stallion was hungry… She would have to remember to apologize extra to Dash later.

“Oh you wish!” The Rainbow quipped, a spring returning to her step. “Okay mister, we’ll get you your snack, come on!”

“No, no, no, no, that won’t do at all.” The pony said with a frown.

“W-whats wrong?” Fluttershy asked, a nervous quiver returning to her voice.

“That’s not my name, I never met anypony called Mister. I don’t suppose I’d remember if I did though, that seems like a terribly forgettable name. It’s all dull and boring-y. I’m called the Doctor, much cooler name. Pleasure to meet you!”

“Oh…um hello Doctor, I’m Fluttershy…” The timid filly replied in her usual soft voice.

“And I’m Rainbow Dash!” The cyan filly added, flying into the air and striking a heroic pose. “Now let’s get you your snack!”

The three ponies crossed over the edge of the forest, their hoof-falls muffled by the layer of detritus on the forest floor. The forest itself wasn’t particularly menacing or creepy, but in the dark each little noise or breath of wind seemed as though it warned of some hidden danger. Fluttershy, despite being in her element, was still on the jumpy side. Occasionally a mouse or other rodent would happen along their way and Fluttershy would ask for the nearest source of berries or particularly tasty flowers. After a few attempts the lanky filly let out a gasp and thanked a particularly chatty possum profusely.

“What was that about?” Rainbow inquired curiously.

“The little possum told Fluttershy that there is a crop of something called… zap apples? Zapples? Zippity do dapples? He was mumbling so it was kind of hard to overhear. They’re about half a mile’s hike that-a-way, in any case.” The Doctor pointed a hoof ahead of himself and slightly to the left. “Also he said he’s been having a rough time with his wife and kids, poor chap.”

The two fillies stared open-mouthed at the grey stallion.

“I speak possum.” The Doctor replied simply, a smile stretching his lips. “Actually I speak raccoon, but they are remarkably similar, really just a slight difference in dialect, so I can just bluff my way on through. Sooooo…. are they special good apples?”

Fluttershy was the first to recover from the Doctor’s latest bout of, uh, eccentric behavior. “Uh… yeah… They are really rare, and supposedly really good, they are more of a myth in Cloudsdale… I’ve never even seen one…” Fluttershy replied.

“But they are supposed to be like super awesome,” Rainbow said, her wings buzzing excitedly once again. “This is so cool!”

“Well then lest get a move on, hop along fillies!” The Doctor trotted ahead of the two fillies who filed along behind him.

Something was nearing her hollow. Three somethings?

‘Maybe.’ She concluded, ‘Either way it will certainly enough for a meal.’

Moonlight glinted off of obsidian chitinous scales as the muscle and sinew beneath them flexed. Claws dug into soft rotted wood, a deep rattling breath was inhaled through a gnarled snout, and the beast began its hunt.

It was beautiful. Undoubtedly and undeniably beautiful. The pale light of Luna’s moon reflected off of the chromatic skin of the fruit. A rainbow-like aurora cloaked the clutch of trees, shimmering and shifting with an ethereal light. The zap apple trees stood in a little clearing, with maybe four or five trees total all growing together in a signal tangled mass of flora.

“Oh. My. Gosh!” Rainbow Dash zipped around the trees in a fit purest excitement and joy, leaving her trademark rainbow in her wake. “Look at them!”

Fluttershy too was enraptured by excitement; she even flew up to one of the trees to collect some of the multi-colored fruit. Gliding down from the tree she distributed an apple to an eager Doctor and waited patiently for Dash to cease her acrobatics. Rainbow landed with a flutter and a flourish and graciously accepted the fruit from her friend.
The three smiled to each other and each took a generous bite.

“That’s amazzzzing…” Dash exclaimed, the static charge of the unprocessed zap apple causing her hair to briefly stand on end.

Fluttershy nodded her agreement, the electric charge momentarily poofing out her long pink mane out into a ridiculous bubblegum afro.

“That’s rubbish!” The doctor exclaimed spitting out half-chewed chunks of fruit. “Okay its official, apples are off the list of Doctor friendly foods, especially one that are all zippy zappy. My tongue feels like electroconversion generator with its temporal shift only half-engaged. Bleah.”

The fillies once more stared incredulously at the strange pony, the action rapidly becoming old hat.

“But… you said you wanted an apple?” Fluttershy asked tentatively, worry lacing her voice.

“Oh. I did didn’t I?” The Doctor began to look a bit sheepish, “Ah, well yes, perhaps I really need oranges, or maybe daisies, or… Hmmm…”

A twig snapped somewhere behind the dark curtain of the treeline.

“What was that?” Dash asked quickly, her attention turning to the source of the noise.

Fluttershy’s breath hitched in her throat. “Th- that’s… probably a bear… we might have woken it up..” Fluttershy took a shaky step toward the edge of the clearing. “Hello little f- friend.”

A low growl responded. Something black and shiny stalked slowly towards the three ponies, the shade of the trees obscuring the Beast’s visage just enough to make it something nigh invisible, something unknown. But what the ponies could tell is that it was big, and likely quite mean.

“What is it?” Rainbow whispered to the Doctor.

“Not entirely sure but you know, just for a lark, how’s about we run away!”

The Doctor and the fillies were running as fast as they could. The Doctor had assured them that they’d be safe if they hid in his box. Personally Rainbow thought this was another bout of the stallion’s madness, but she knew that was where they had parked Fluttershy’s miniature cloud. If she had any hope of getting her and her friend home to Cloudsdale, she would need it.

There was a loud crash somewhere behind them, then a roar. Whatever it was behind them wasn’t particularly happy that they had decided to run. The noise startled an already nearly petrified Fluttershy, the ice cold talons of fear lancing her heart anew. However, that same fear kept her legs moving, the adrenaline coursing through her veins propelling her forward recklessly.

Rainbow Dash’s wings itched. She wanted to be flying, not running, she needed it. As the trio barreled forward the Doctor nearly clipped his head on a low hanging branch, violently reminding Rainbow of why flying in a dark forest would be a bad idea. She groaned from the effort her little legs were exerting. This was the one time in which Dash briefly wished she could swap places with Fluttershy whose long legs would be an asset in this crazed sprint.

Another crash, then another, then another. The beast clearly had no regard for the trees that blocked her path.

The ponies finally reached the edge of the forest and Rainbow Dash shot ahead of her companions as fast as her little wings could carry her. She scooped up the little cloud and met with the others just as they reached the strange blue box.

“Fluttershy hop on! We can go get help for the Doctor, maybe a guard or something can carry him.”

Fluttershy hesitated, “But… what if they don’t make it…”

“We have to go, and I’m not leaving you!” Rainbow shouted.

“Girls, it’s okay. Give me a half-a-moment and I’ll bring the old gal around.” The Doctor said as he climbed onto his box.

Once on top of it, he hopped through a hinged opening that looked like a door. The fillies could just make out a faint call of “Geronimo!” echoing forth from the opening.

“What is he-” Fluttershy began before being cut off abruptly by a loud mechanical whooshing. There was a gust of wind that caused the fillies to shield their eyes, and when the gust subsided the fillies stared in awe at the place where the smoking box once sat. ‘Once sat’ being the operative words, because now there was nothing but a patch of disturbed earth. No box. No Doctor.

The fillies looked at each other, and though they no longer heard the crashing of trees Fluttershy still scrambled onto the cloud with frightened urgency. Where ever the Doctor had gone, at least he was safe now.

“Smoke! Icky, icky smoke!” The Doctor spoke aloud to himself as he managed to land the TARDIS. Fighting through the acrid haze, he galloped to the door calling out ahead of him as he went. “Rainbow Dash! Fluttershy! I’ve got it! Don’t mind the smoke I can get us somewhere…”

The Doctors voice fell away as he exited his vehicle, and squinted in the midday sun. “…safe…”

A deep sound like the tolling of a bell intoned from the TARDIS’s interior. “Oh no, not now!” The doctor knocked on the door with a fore hoof, “C’mon, I know you’re all sick and what not but can you hold off on the repairs just a bit longer?” The cloister bell sounded again in response, and the Doctor puffed out a sigh. “Oh well then. You just… just sit there, and I’ll be back, yeah that’s it. Don’t go running off!”

The Doctor turned and faced down the small alley in which the TARDIS had parked itself. The alley itself appeared to be just off a bustling market street in a small town. Or so the Doctor guessed, these things couldn’t always be taken for granted in Doctor’s travels. A stray newspaper blew past the Doctor’s hooves. The slate stallion deftly picked up the paper (apparently titled “The Foal Free Press”) and read a byline proclaiming the coronation of a new alicorn princess.

“Huh….” The Doctor exited the alley and entered the market, peering about in wide eyed wonder. There were stalls selling all kinds of fruits, grains, vegetables, arts and crafts, and really just about anything you could fit into a stall to sell.

“Oh, oh I recognize you now! Ponyville, splendid, I love Ponyville!” The Doctor grinned from ear to ear, but then his features fell slightly a look of puzzlement flashing across his face. “But… I didn’t mean to come to Ponyville… I was just trying to jump upright near Rainbow Dash and Flu-”

The Doctor’s musings were cut off by the sound of a shopping basket crashing to the ground somewhere close behind the grey pony.

“D-Doctor!?” Squeaked a strangely familiar voice.

Author's Note

Here's Chapter 1. I've got 5 or so chapters planned out for this 'episode.' I had no Idea the response would be so amazingly overwhelming! Thank you all, and here's hoping I can live up to the hype.

Enjoy!

Chapter 2

Chapter 2

“Oh…Oh I’m so sorry…” Fluttershy spluttered as she bent down to recover her shopping, using her declined posture as an excuse to hide between flowing pink mane. “You… just reminded me of... oh… n-never mind…”

How could she have let that slip? He was never real. No pony, no magic blue box, no scary monster. It was just a romp in the forest that had gotten her and her best friend into trouble with their parents a decade and a half ago. But all the same… This pony looked just like him; even down the acrid smell of smoke in his mane. She smiled to herself, now she knew it was all just a mistake.

‘Just some silly sense memory, or one of those things that Twilight is always going on about, he just smells like smoke is all,’ she thought to herself. A sigh of relief escaped her lips, but after a moment she arrested in renewed panic. ‘W-wait… how can I have a sense memory of an imaginary friend?’

She chewed on her lip. No. Couldn’t be. It was impossible. Fluttershy began to lift her gaze, the sounds of the marketplace seemingly falling away.

A pair of wide, pale-golden eyes invaded her field of vision as the stallion brought his face mere inches from the pegasus’s own, “You look familiar, have I met you before? Wait don’t answer that .‘Cause I can’t have met you yet , you see. I’m new. Very new, well sorta very old too, but also very new. Barely done cooking, as it were. Underdone and half-baked that’s me…” The Doctor finished his rambling and then returned to staring at the mare with a single brow arched and a searching gaze. “But you called for a doctor? Are you hurt?”

Fluttershy squeaked. She had witnessed wonders in her time as an Element of Harmony, but this… this was too strange. With no small effort of will she forced her voice past her lips, “Doc- …Doctor?”

“Uh sure you’re okay? I can get someone…” The Doctor said, withdrawing his face and continuing his study of the buttery mare. There was something oddly familiar about her. Pink mane… creamy yellow coat… aquamarine eyes…

“Look I uh, I forget which way it is to Cloudsdale,” The Doctor continued. “I think I may have given a couple fillies quite the fright last night and I want to see if they are okay… oh blimey, I don’t have wings do I?” The doctor quickly turned in a circle trying to examine his own back. “Nope, not this time. Oh I hope I can find a balloon or-”

The Doctor abruptly cut himself off with a facehoof. “Ugh, thick silly Doctor. Thick, silly, and old. It’s you isn’t it?”

Fluttershy managed a nod.

“The yellow filly?”

Fluttershy nodded again.

“Too long legs and friend with a rainbow mane?”

Fluttershy nodded once more, though a light blush tinged her cheeks.

“Oh yay, that’s wonderful!” The Doctor cheered. “You’re safe! I was just about to go back, but I guess I can’t now.” The Doctor’s brows crinkled slightly. “You know, that’s probably a fixed point now…”

“Fixed…what?” Fluttershy said her quiet voice again faltering.

“Well you see time is all bits and bobs. But a few of the bits are more bitty than the bobs… it’s all very…” The Doctor thought for a moment before concluding with comfortingly familiar explanation. “Timey-wimey,” He pronounced with a solemn nod.

Unfortunately this still left Fluttershy without a clue as to what the strange pony was talking about. ‘Something about the time?’

“Um…It’s about noon?”

The Doctor looked blankly at Fluttershy for a moment before a wide grin split his lips. “Are you asking me to lunch? I’d love to. We never did get anything after the apples!”

Fluttershy blinked several times, still not sure what to make of the pony standing before her. However, it seemed her instinct for politeness ran deeper than her misgivings, and she decided to oblige the Doctor.

“Sure, I was just on my way home.” The shock of the encounter had begun to finally subside, and her voice now quivered no more than usual. “I’m sure I can make us something.”

Fluttershy entered her cottage with the Doctor close behind, with her shopping carried in his mouth.

“I told you, you didn’t need to do that…” Fluttershy began as the Doctor set the bag down.

“Nonsense, I’m the Doctor and I’m here to help, and sometimes carrying shopping is helping.” The Doctor replied as his eyes darted around the cottage, taking in its numerous bird houses and the scampering of a few rodents across the floor. Fluttershy’s cottage was the very picture of activity, especially now that Fluttershy had returned home. Waves of birds flew down to greet her with excited chirps, mice and chipmunks scampered around her hooved, waving hello as they passed. Fluttershy, ever in her element among her woodland friends, responded in kind to each salutation.

The whole pageant had a heartwarming quality to it that brought a smile to the doctor’s lips. That was until a half chewed carrot was expertly bounced off the back of his skull. “Ouch...”

Fluttershy was snapped out of her happy reverie by the cry of pain. She wheeled around to see Angel readying another piece of vegetative ammunition.

“No, no, Angel. He’s a friend, promise.” Fluttershy said, floating over to her pet bunny with a deft movement of her wings. “A very old friend and he is very nice. You’ll see. And mommy is going to have him over for lunch.”

Angel looked over to the doctor and made a series of swift and deliberate movements that more or less translated to: ‘watch your step.’ Then looking back to his caregiver he mimed the action of looking impatiently at a wrist watch.

“Oh yes Angel, I’ll get you your lunch in a moment.” She said turning away from the little white rabbit – who was still miming frantically - and back to her guest. “I’m so sorry, he gets very protective around strangers. Here let me take a look at that for you.”

“No worries,” The Doctor said with a smile, “I know how unruly a companion can be.”

Fluttershy inspected the back of the doctor’s head, using her hooves to part his mane and inspect for any swelling. “That’s odd, there’s nothing there… The last time Angel threw a carrot that hard, Dash had a black eye for weeks…”

“Oh, that’s my fault. Sorry, still in my first fifteen hours I think, so hurray! No bumps, no scraps, and occasionally a new hoof!” The Doctor said enthusiastically.

“First fifteen hours of what?” Fluttershy inquired softly.

“Of my life I suppose,” He with his usual exuberance, “or of my life with these eyes at least. New face, you see.”

Fluttershy felt more lost than before. ‘What did he mean by a “new face”? How could a pony have a new face?’ She decided to try not to think about it and quickly busied herself with the preparations for their lunch.

A pot of tea and two daisy sandwiches later, the two ponies still continued to sit and talk cordially. The Doctor didn't say much of substance, but his bright-eyed liveliness more than made up for it. He proved amazingly curious about current life in Ponyville (“As it is now” is how he put it) as well as current political affairs. He would often make odd little comments too. For example when Fluttershy explained her friend Rarity’s latest style innovation (the fashion sock) the Doctor saw fit to add:

“Always wondered who did that, thought it was going to be me.”

Soon Fluttershy found she was talking more and more about herself, finally arriving at her position as one of the bearers of an Element of Harmony.

“Oh, oh my! You’re that Fluttershy are you?” The Doctor said, sounding impressed.

“What do you mean?” The timid mare squeaked, “…There are others?”

“Oh blimey yes, it becomes quite the popular name!” The Doctor replied beaming.

“I’m sorry but…” Fluttershy began, unable to contain her curiosity any longer. She had an idea, a crazy theory really, but it may well fit a crazy pony like the Doctor. “I don’t understand, Dash and I met you fifteen years ago…and you don’t look any older...and you still smell like smoke. How did you get here?”

“Took a shortcut.” The Doctor said proudly.

“I know Twilight said it was possible… but…you’re not a unicorn.” Fluttershy decided she might as well come out and ask,

“How does an earth pony time travel?”

“In a box,” The slate stallion replied, “And it’s a wonderful box at that, but trust me, you’ll be seeing plenty of it.”

However in that moment the door to the cottage burst open, and a very irate cyan pegasus flew in.

“What’s is going on here!?” The rainbow-maned mare spoke quite forcefully, a bit growl in her voice. “First you stand me up for our lunch-”

‘Angel was trying to tell me I was going to be late…’ Fluttershy mentally chided herself, but the Doctor’s arrival had forced all else from her mind.

“-Then when I come by because I think you might be in trouble, but here you are chatting up somepony who wants to show you their box!?” Just as it seemed Rainbow’s anger couldn’t mount any higher, she heaved a massive sigh. Her posture slumped, all bluster seemingly gone.

Fluttershy immediately made her way over to her fillyhood friend, laying a comforting hoof around her neck. “Rainbow, it’s not like that I promise…I’m so sorry I forgot our lunch…And... um, I know he has a long mane, but that’s a stallion…”

The cyan mare perked up a bit, but she still seemed a little hurt. “Well, what’s he doing here then?”

Fluttershy took a deep breath; this was not going to be easy. “He’s the Doctor…”

Rainbow Dash’s face immediately filled with concern. “Flutters, are you okay? Are you sick?”

She began to examine and prod at the yellow mare. “Is it your wings, or your eyes, or are catching a cold?” She then turned her attention to the Doctor. “What’s she got? Will she be okay?”

“She’s sick? Oh dear no this won’t do, she’s not supposed to be sick.” The Doctor rose from his seat and began to join in examining Fluttershy. “Oh I hope she’s okay.”

Fluttershy’s world quickly became that of prodding slate and cyan hooves. They checked her reflexes, temperature, visual acuity, glands, and half a dozen other procedures of checking to see if somepony is feeling well.

“…Dash…”

“What do you mean you hope? You’re the Doctor!”

“I know I am.”

“…Rainbow…”

“So you should know if she’s sick!”

“How could I know that?”

“Dashie!”

The two ponies ceased bickering and quickly turned their attention to the usually quiet mare.

“He’s the Doctor.” She said slowly, placing weighty emphasis on the word.

Rainbow looked at her blankly. As Fluttershy’s meaning slowly dawned on her, her eyes widened. She looked at the Doctor, then back to Fluttershy, then back to the Doctor.

Then her face began to brighten, a wide silly grin gracing her features, “I told you he was real! I told everyone he was real! I’m glad I bit those psychiatrists.”

Fluttershy smiled, but still hid behind her mane a bit, embarrassed. “I’m sorry I ever doubted you…”

Rainbow embraced the buttery pegasus and gave her a zealous and passionate kiss on the lips. The timid mare returned the gesture, blushing a deep scarlet. The sight of the intimate action caused the Doctor suddenly looked quite squeamish and awkward. Rainbow simply smirked at the sheepish stallion.

“You’re worse than AJ’s Granny Smith,” The cyan mare said with a snort. “’Just ‘cause you two mares done finally got together doesn’t mean ya gotta be neckin’ round tha clock.’” Dash added in her best imitation of the old mare.

“I’m the Doctor, and I’m worse than anypony’s Granny Smith,” The Doctor said sternly, though still looking a bit uncomfortable. “The two of you were fillies less than a couple hours ago.”

“What do you mean a couple hours ago?” Rainbow asked incredulously.

“He’s… a time traveler…” Fluttershy added quietly.

“Whoah really?” Dash queried animatedly. “That’s so cool!”

“You bet it is!” The Doctor exclaimed.

Elsewhere, deep within the Everfree forest a breeze stirred the air outside a large earthen warren that rested beneath the roots of an ancient uprooted tree. A curious squirrel poked its head into the gaping maw of the burrow. Gingerly it moved forward into dark gloom, tiny paws landing noiselessly on the soft earth.

A ragged inhale stirred the air. The squirrel froze, hoping it hadn’t been seen by the inhabitant of the cave. Unfortunately, seen or unseen it mattered little. Before the squirrel could so much as squeak, a set of razor sharp jaws closed around it with a sickening crunch, devouring the little critter in a literally a single bite.

The beast sighed as it swallowed the hapless woodland creature. A little morsel, that’s all the squirrel had been. The beast desired a meal. It took a deep breath preparing another dejected sigh, when it abruptly froze. There was a scent on the air. The scent of a lost quarry from another time, from another place. One part fresh meadows, one part the smell of ozone after a lightning strike, and one part acrid smoke.

The beast smiled, or at least the nearest thing to the expression that the monstrosity could manage. Perhaps there would yet be a meal this day.

Author's Note

Just thought I'd add, in case it didn't come across as such, I am not implying Granny Smith is homophobic, rather she's just old fashioned about affection in public.

Chapter 3

Chapter 3

“So let me get this straight,” Rainbow Dash’s voice was hushed, her eyes narrowed in skeptical inspection of the pony seated across from her, “You are over nine-hundred years old, are the last of an alien pony civilization, you speak ‘everything’, you have a time-machine/spaceship that looks like a blue box, and routinely bring along ponies to serve as your companions.”

“Yeeeaaah, that’s about right.” The Doctor replied, ever enthusiastic.

“That. Is. So. Cool!” Rainbow said letting out an uncharacteristic squee of excitement.

As the sun sat behind them, the breeze that had played gently with their manes began to develop a cool edge. The trio of ponies had decided after their reunion at Fluttershy’s cottage that perhaps they should have a nice little night on the town to celebrate. Rainbow had suggested several of Ponyville’s more renowned cider-pubs, but – much to her disappointment – the Doctor expressed distaste for the alcoholic beverage. Fluttershy had then suggested the café where Rainbow and she had planned their ill-fated lunch date. Dash was quick to agree, seeing as the café was home to “the best oat-burger in Equestria”, or at least that was the flyer’s not so humble opinion.

Now the trio sat outside in the café’s open-air patio chatting away; two marefriends discovering all they could about the enigmatic, once-thought-imaginary stallion seated before them. The Doctor for his part was quite happy to respond, regaling the pair with tidbits of knowledge and trivia learned from his extensive travels.

“It is cool isn’t it?” The Doctor said with a smirk, running an idle hoof through his sleek mane. “Best way to get around the cosmos, my TARDIS. But you lot already knew all you really need to about yours truly. The rest there is just sort of the sprinkles on the cake. I’m a mad pony with a magic box. Now you two, there’s a real mystery! How did you two get all…” The Doctor struggled momentarily attempting to find the proper words. “All, you know…” The Doctor made a kissy face to complete his question.

The sight of the stallion’s use of pantomime sent Rainbow into fits of howling laughter, and Fluttershy even tittered politely behind her hoof.

“S-sorry,” Dash said still shaking with laughter. “But you’re a grown stallion, are you sure you’re nine-hundred and not nine?”

“Well, it’s all very complicated with you ponies isn’t it?” The Doctor said, unsuccessfully attempting to keep a blush from appearing on his features. “How am even supposed to know what all-” he waved a hoof at the two of them “-this means.”

Fluttershy offered a kind smile to the Doctor. “It’s okay Doctor.” The timid mare shot her marefriend a not so subtle look, and Dash’s fits of giggles soon subsided. “We’re, um, dating or I supposed engaged really. We were always friends and then, well, someone suggested that we get together. I mean we were both thinking it, but didn’t know the other was too…”

“Yeah, I mean, it’s kind of amazing how you can feel so strongly about something but be so oblivious, you know? We were always so close but we never saw what was right in front of our muzzles. Okay, plus I admit I always sort of thought she was into stallions.” Rainbow added her voice a bit sheepish. Fluttershy gave her marefriend a warm nuzzle. “But boy was I wrong about that last part.”

The display of affection seemed to fill the Doctor with a mix of both heart-warming and uncomfortable feelings. He muttered something that sounded and awful lot like “Ponily-wonily” before directing his focus to the town around him.

It always brought forth the thrill of excitement to see Ponyville. So much had happened here, so much will happen here. And then there will be New Ponyville, Spaceship Ponyville, even a planet named Ponyville. The Doctor could look around and see all that was, all that is, and ever could be. He knew it was all so fragile, so precious, like spring snow. It could all change, time could be rewritten just like… wait he was an equine life-form so he didn’t have fingers to snap… so what did ponies do instead? Where had he even picked up that turn of phrase?

“Doctor, are you okay?” Fluttershy ventured forth quietly. The Doctor was now staring intently at a hoof, jerking it ever so slightly in one direction, then another, and every so often holding it up to his ear.

“Leave him,” Dash whispered to her lover, “While he’s distracted maybe we can get a little more-” She parodied the Doctor’s kissy face “-done.”

Fluttershy playfully nudged Rainbow in the shoulder with a hoof, playfully chiding her for making fun of the odd stallion. Dash decided to try her luck and leaned in for another kiss. The pair shared the affectionate gesture with equal fervor, while the doctor still examined his hoof.

More scents, more meals. The entire area war swarming with them. The fought the overwhelming nature of the sensation and attempted to stay focused at the task at hand. This was more than a matter of feeding. This was a matter of pride.

The beast moved slowly. The warmth of the sun upon its scales had vanished, replaced by the cool touch of night. This was good, for the beast knew that in the absence of the light given off by the day-star its obsidian form became harder to detect. The beast continued its prowl, hugging tightly to the walls of the shops and homes in this new urban environment

The Doctor gave a little cough, and the pair of pegasi interrupted their kiss.

“You two sure do that a lot, don’t you?” The Doctor inquired, his voice somewhere between innocence and annoyance.

“Hey don’t knock it ‘til you try it,” Rainbow responded with a laugh.

The Doctor frowned slightly, more in concentration than displeasure. He took in the sight of the two pegasi, examining them with careful consideration. He’d had stranger companions, surely, and more than one pair had taken to falling in love in his care...

Unfortunately the Doctor was brought forth from his reverie prematurely when out of the corner of his eye he spied something that did not belong in Ponyville. No, not in Ponyville, not in Equestria, not on this planet.

“Fillies?” The whole of the Doctor’s disposition changed. His eyes began to dart around dart around nervously searching for the quickest avenue of escape. “Have either of you ever seen a Jihaxian super-predator before? Does somepony around town maybe keep one as a pet?”

“We aren’t fillies anymore,” Rainbow mumbled under her breath, but both she and Fluttershy shook their heads in response to the doctor’s question.

“Then might I make the humble request that we run.” As he spoke, the Doctor rose slowly from his seat. The pegasi mirrored his actions but as they got to their hooves they heard a thunderous growl. They turned to see the indistinct shiny obsidian form of the horror that had stalked their nightmares sonce their fillyhood adventure.

Of course, if the Doctor was real, so were the monsters.

The Doctor turned and began to bolt. “Run, Run-” Suddenly the Doctor became aware of the odd sensation of his hooves leaving the surface of the road, “Run?”

“How about we fly instead?” Dash said with a bit of a laugh as she and her marefriend supported the flightless pony.

Below them the beast took a deep rattling inhale, searching for its quarry. It would not let it escape, not this time…

Author's Note

Sorry for the shorter chapter, just sort of teeing things things up for the climax. Figured I'd also give a small window Fluttershy and Dash's history as a couple. Still not sure if I will do the whole River Song Story line, but I figured I'd leave myself open to it by subtly incorporating a bit of the "Let's Kill Hitler" Amy & Rory history into Flutters and Dashie's back story as a couple.

Chapter 4

Chapter 4

The pair of pegasi deposited the Doctor on a roof top half-way across town.

“What are you doing!? We need more distance! Now!” The Doctor’s usual energy had been diverted from bubbly and charming to frantic and manic. “That thing does not stop. It doesn’t rest, not until we are swirling about in its gut!”

Fluttershy cowered at the Doctor’s words. Rainbow Dash immediately stepped in front of her lover, shielding the shy mare with her own body.

“Shut up!” Dash spat. “First off, you might not realize how taxing tandem flying is, but it’s not easy! Add in a passenger and it’s even rougher! Second, Flutters isn’t the strongest flyer and you scaring her isn’t helping!”

The Doctor stood his ground- or roof, as it were - and took a step towards the cyan mare

“That thing down there could slaughter this entire town should it decide that’s the best way of flushing us out. The Jihaxian super-predators are merciless, prideful killing machines. They live for the hunt and the hunt alone. They live to kill, to consume, and spend their entire adult lives hopping from ecosystem to ecosystem. We’re lucky, we must have wounded it’s pride when we escaped from it all those years ago, so for now its focusing on us, but if we don’t lead it out of here soon we won’t be the only ones on the menu.” The Doctor’s tone was urgent, yet measured.

Rainbow cast a backwards glance at Fluttershy, worried about how the frankly frightening revelations would affect her marefriend. It was as Dash had feared, the buttery mare was shaking and her eyes had widened with fear.

“M-maybe… I could… try to talk to it?” Her voice was quivering and quiet. Maybe if she could just show the beast some kindness, she had done it before. There was the manticore, and the cockatrice, and-

“No,” the Doctor replied firmly.

“Then what the buck are we supposed to do!” Rainbow shouted again, though the volume of her voice didn’t completely mask her growing sensation of dread.

“I told you, we run, fly, whatever we can. We get clear of town.” The Doctor’s face had become hard. Only a few hours into his current iteration and he was already facing down a nightmarish foe, and what was worse if that he was endangering the two fillies… no… the two mares whom he had first met.

“…and then?” Fluttershy squeaked timidly.

“I’ll think of something” The Doctor said, before adding with a reassuring smile. “Trust me.”

The trio had reached the edge of town by way of another short flight, but effort had severely taxed Fluttershy’s underused wings. The Doctor directed the pegasi towards the Everfree Forest with an outstretched hoof, and the three ponies began to sprint as fast as their legs could carry them.

Dash was about to question the Doctor’s choice of havens when the she felt the bottom drop out of her stomach. A deafening roar erupted from behind the fleeing ponies. Rainbow dared not look back, though. It easier to put on a brave face when she wasn’t constantly looking back at the obsidian form which had assaulted her dreams in ages past.

‘No, it can’t be just an act. I am brave! Fluttershy needs that to keep going and I’d rather be banished to the moon than let my doubts keep that strength from her!’ Rainbow thought to herself, as the three ponies crossed the tree line.
Suddenly Fluttershy planted her hooves in the soft soil, wheeling about to face the oncoming horror.

“What are you Doing!?”The Doctor called out.

“Flutters!” Rainbow cried urgently.

“…no… no I can’t let it hurt anypony…” Fluttershy whispered, more to herself than her companions. “…can’t let it hurt Dashie…I can stop it…”

The beast had begun to charge, its delicate nostrils had noticed that the scent of its prey had begun to grow stronger rather than fade. ‘So the prey has decided to face death. Noble.’

“’Shy!”

“I can end this!” Fluttershy shouted, tears pooling in the corners of her eyes.
The timid mare held her breath, her eyes narrowing to angry slits as she began to give the alien predator the Stare.

“How. Dare. YOU!?” She screamed at the chitin-armored beast, the force of her voice tearing at her throat. “How can you hunt ponies like this!? We did nothing to you! Just-… Just leave us alone! You… You big-”

She felt her own sharp inhale of breathe cut off her tirade. The empowering aura of the Stare left her. For the first time she could see the beast clearly as it closed the remaining gap between them. The beast that she had thought could not get more horrifying charged towards her, and she could for the first time see its ghastly face.

Its blind, eyeless nightmarish mask of a face.

Fluttershy screamed. Panic gripping her as she realized she would face her death shaking in fear.

A strong hoof hooked around her midsection and she felt herself pulled backward into the forest. Rainbow was flying low to the ground, her marefriend on her back, dodging low lying branches and tree trunks. The Doctor ran beside her, strong earth pony legs – and a spare heart – allowing him to just barely keep up.

There was a crash behind them as they heard the beast barrel into a tree. Then another. Then another. A howl of purest rage pierced the cool night air, as frustration welled up within the creature. It hated forests. It longed for the flat plains of its home planet.

The trio stopped for half a second to allow Fluttershy to get back on her hooves. She had tears trailing from her eyes, but she nodded resolutely and the three continued on.

“You should have told us it was blind.” Rainbow growled at the Doctor as they plowed on through the forest. “Fluttershy could have been killed!”

“There’s no time.” The Doctor replied, his voice rising a bit in frustration.

“Tell me you have at least thought of a plan?”

The Doctor remained silent for a moment. Slowly an idea began to dawn on him.

“Yes… Yes I think I do.”

The beast felt another tree snap before its sinuous form. The dense growth of the forest was nothing that the beast couldn’t shrug off, but the effort stole precious moments. The beast bumped into another tree, powering through it and reducing it to splinters.

Suddenly the scents of his quarry began to intensify.

‘Close. They must be close now.’

Despite this the beast was wary. It had been convinced that perhaps the prey had chosen to die in a manner as honorable as could be expected from prey, but the shame of this game apparently knew no bounds. To face death and flee, there was no greater dishonor.

The beast drew another of its ragged breathes through its sensitive snout. The intensity of the scent remained unchanged.

“Hello there.” A voice called out to the beast. “I think you have chased your prey long enough.”

“” The beast replied in its own native tongue. To the ears of the two mares it sounded only as indecipherable grunts and growls, but the Doctor, the last of the Time Turners, the stallion whose race was ancient before the star that Jihaxis orbited even winked into existence, The Doctor understood every word.

“Do you miss your home world? I can take you there you know. I can take you away from this planet and back to your kin.”

The voice with which the prey spoke held no fear; if it was lying the beast could not tell. The prospects was indeed thrilling, to leave this backwater planet and return to the glorious plains of Jihaxis. Such an offer seemed beyond belief, yet the confidence with which the prey spoke told the beast that it was indeed within its power.

“All you have to do is let us live.”

“” The beast replied as it coiled its muscles, gathering all its strength and preparing for the final strike. “”

And with that, fate was sealed. The beast leapt forth, pouncing with all the might it had garnered from its many hunts. Its claws whistled through the air, seeking the soft flesh of the prey.

The Doctor breathed a sigh.

“Now!” He shouted and the two pegasi flew off in opposite directions, leaving the earth pony alone on the narrow rope bridge that spanned the deepest canyon in the Everfree Forest.

As the beast came down upon the spot where it thought its prey had been, it tore through the rickety structure like it was tissue paper. The claws that had been meant to mutilate its prey were now the instruments of its own demise as they severed the taut ropes that held the bridge aloft.

The Doctor had begun running for the other side of the chasm before the bridge had lost its tension, but he hadn’t been quick enough. He too was tossed from the rotting planks of the bridge, down into the gaping maw of the canyon whose jagged rocky floor waited for him below.

‘Well…’ he thought with a slight smile, ‘…this has certainly been my briefest regeneration…’

Suddenly, once more he found himself hovering in midair held aloft in the forehooves of two pegasi.

“If you’re going to make a habit of this, I’d recommend losing some weight.” Rainbow Dash said with a grin.

The trio had returned to Ponyville later that night. They were exhausted, bruised, and Fluttershy in particular had an extraordinary amount of twigs and leaves in her mane and tail. Despite all this however, they were victorious. Though

Fluttershy herself had been too squeamish to inspect the grisly sight, Rainbow Dash had confirmed that the creature had indeed not survived the fall.

The Doctor had told her that it hadn’t been necessary, but Rainbow needed to be sure. At first she had told herself it was for Flutters, all to make her feel better, to assure her that it could never come after them again. About halfway to the canyon floor Rainbow realized that she was lying to herself, that she needed the proof as much as Fluttershy.

The sight had indeed been every bit as gruesome as Rainbow had expected, but it truly was proof positive of the creature’s demise. She was free. The monster was dead. She was safe. Fluttershy was safe. Her nightmares had been real, but now they were really over.

The trio pulled up to an alley off Ponyville’s market street. Tucked into a little corner, was the Doctor’s TARDIS. It was the first time the pegasi had seen the thing standing upright, and for some reason it just seemed much more, well, undamaged. It was true though. The paint was a deep blue, no longer scorched or cracked. The windows were no longer shattered but instead stood whole.

“Hello old girl.” The Doctor said, rubbing the corner of the box with genuine affection. “Let’s see what you’ve got for me this time.”

The Pegasi then stared as the Doctor tapped a hoof on the ground and the door to the box opened revealing an impossibly large interior.

It was beautiful in a way that was all its own. The walls filled with odd holes here and there, some cosmetic, others appeared to function as windows, while still others appeared to lead to other parts of the TARDIS. Walkways and sets of stairs too lead this way and that off of the main room, and in the center of it all was the main console.

It was both wonderful and baffling. It glittered with various blinking lights, not unlike several of the machines the pair had seen Twilight fiddling with from time to time. However unlike Twilight’s machines, the console appeared as though somepony had scattered a foal’s toys across its surface, and then glued them in place. Yet somehow the whole thing still made sense.

“What do you think?” The Doctor said as he stepped through the threshold, casting a backward glance at the two mares.

“Its…um…bigger…” Fluttershy managed, astonishment plain in her voice.

“…On the inside.” Rainbow said, finishing her marefriend’s thought.

The Doctor simply smiled as he turned and waved the pair inside. “What are you waiting for, then. Come along ponies.”
The mares looked to each other.

“But… Dashie tomorrow is…” Fluttershy whispered.

“It’s a time machine Flutters. As in we can go on and be back in five minutes.” Rainbow said with a comforting hoof placed about the timid mare’s shoulders.

“O-okay…if you’re sure you want to…”

“It’ll be fun! We can see the universe. You’ll get to meet all kinds of new critters and we can go on all sorts of adventures.” Dash gave the buttery pegasus a peck on the muzzle. “Together.”

Fluttershy felt her cheeks heat up a bit as a smile curled her lips. “Okay Dashie, let’s do it.”

The Doctor had taken up the controls, and smiled as he saw his new companions cross the threshold.

“Close the door after you’re in, and wipe your hooves. The TARDIS isn’t all that fond of muddy floors.” The Doctor then threw a switch and the engines began to engage, “Alrighty. Rainbow Dash, Fluttershy, hold on tight! Next stop: Everywhere!”