Doctor Whooves and The Triarch Colony

by gcsmith

Rating: everyone
Tags: My Little Pony: Friendship is Magic, Doctor Whooves, Adventure, Crossover, Main 6
Length: 4657

The Doctor is at it again, saving lives and running away. In fact mostly running away. However this time he has to deal with it all with a brand new body in a world he doesn't know.

Mysterious events are occurring as several ponies have gone missing, their homes left abandoned and in states which seem like they haven't been lived in in a long time. Can the Doctor do this without bringing destruction to the sleepy town he has landed in.

Grammar Checks performed by Deathtap

Published 2012-06-10 14:04:02 UTC
Last updated 2012-06-19 13:46:35 UTC

Prologue

The summer day was coming to a close, shops were closing and everypony who wasn't otherwise preoccupied was heading home. This was true for Hay Stacks, the sand coloured stallion was heading home after a long day in the fields. He had spent the day working at the Baarbury family farm. It was hard work, but as his three-hay-bale Cutie Mark reminded him, no one around could work hay like him.

He waved to the ponies he knew on his way home, passing Berry Punch and Strawberry Squash who seemed to be in another heated debate about the best way to store their beverages. He chuckled, they had been arguing since they day they decided to quit the competition and join their businesses. It didn't do much for their social interactions but their business boomed and soon Berry Squash brand products were in every major store in the town, rumor had it that some big shots in Manehatton were interested in buying into it. Still Hay Stacks gave the rumor mill no heed, he was a simple pony and preferred his life simple and quarrel free.

It was as he turned into the quiet street at the edge of town where his house stood that he heard a strange clicking noise. He paused for a second and looked around, but saw nothing. He shook his head and carried on. The street was usually quiet but strange noises weren't uncommon, after all you can't live in the same town as that strange pink baker mare and not expect some kind of commotion once in a while.

Clopping up to the front door he placed his key in the lock, it was as he turned it that he heard that strange noise again. A rapid click, almost metallic. He spun around and studied the street, scratching his head. It was empty; where the hay was that noise coming from?

"Anypony there?" he called out, but got no response apart from a few of the curtains moving in the neighboring houses' windows. 'Must be your imagination Hay Stacks, probably too much sun or that salt lick you had at lunch time.' he thought to himself. His mother had always warned about the dangers of salt lick. Not that he minded, a temporary harmless clicking noise was a small price to pay for the short high the salt lick gave. Realizing it was probably all in his head he opened the door, retrieved his key and prepared for a quiet night.

A couple of hours later Hay Stacks was taking a long and well deserved soak in the bath, letting the hot soapy water wash his aches from the day away. He was just admiring the multicolored bubbles of a special blend of bath salts he had be sent by a distant cousin from Trottingham and relaxing in their scent when there came the sound of a smash from down stairs.

"What In tarnation?" the stallion asked looking confused, he lived alone and he had never had problem with vandals or break-ins in this street in all his ten years living here. Grumbling he tore himself away from his soapy pleasure, wrapped a towel around his midsection and walked downstairs to investigate.

Upon entering the living room he could instantly tell from the cold air what had happened, and his suspicions were confirmed when he eyed the broken window, his curtain fluttering in the new found breeze. Carefully, so as to avoid stepping in any glass, he trod over to inspect the damage.

"Hmm, that should be easy to repair," he muttered to no pony in particular. The damage to the window was minimal, barely a ten centimeter in diameter hole was present in the glass. He was glad it was so small since only one pane was damaged, that would stop the costs from being high at least.

The next thing to do was to work out what had caused the broken window. Shards of broken glass littered the floor nearby so that meant the window was broken from something outside coming in, but there was no stone nearby - nor was there the sound of a small critter or bird. It was truly puzzling.

Hay Stacks sighed and turned to head back to his bath, determined to soak in its pleasure while it was still warm when he was stopped in his tracks by a noise. The was a click like earlier, however this time it was louder, no not louder closer. In this very room. Moving to turn on the light the clicking occur ed with every step of his hooves, as if something was keeping track of him. Sweat was starting to trickle down his neck as he reached the switch and nervously he flipped it from the off position to on.

Turning around the room was empty, the broken window the only sign of anything amiss, even the clicking had stopped. Hay Stacks relaxed, his overactive imagination was playing tricks on him still, obviously the salt lick hadn't quite left his system. He turned off the light and took a step out into the hall, his hoof crunching on something as it landed. Nervously he looked down and was met with a set of glowing red eyes.

The peace of the Ponyville night was broken by a piercing scream for but a second, then all was silent again.

Chapter 1 - Falling without Grace

The Tardis was burning. Fire was everywhere and the Doctor was dancing around the controls like a mad-man, well more like a mad-time-traveling-alien-with-two-hearts-and-whom-had-saved-the-universe-multiple-times-instead-of-man, but he was definitely mad. He grabbed a hammer from a nearby rack and smashed it against the side of the console, "Work will you please?!" he half urged and half shouted as he checked over his shoulder. The remains of a Dalek was sat to one side, its armour smoking and its electronics sparking. It was out for now but the Doctor knew it would be repaired before long.

The Doctor exchanged his hammer for a polymoprhic telthus four... in other words a spanner and nipped below decks. Undoing some bolts he threw the spanner to one side and pulled out his sonic screwdriver, he changed the setting of his trusty tool and thrust it down into the depths of the ship activating it near a series of light bulbs attached to a piece of dull piece of steel covered in wires and pipes. The screwdriver whirred and activated some hidden piston and the bulbs started to flash. To the untrained eye it would look like a piece of junk, but to the Doctor it was a thingamebob or a wotzit, whatever it was he needed it now to save himself and the Tardis.

The Doctor wrenched the working device from its resting place and climbed back up to the console. He connected the two together with a random assortment of multicolored wires, which would again appear to an outsider to be at random, but to the Doctor was exactly what was needed. He hoped.

Behind him the Dalek's weapons started to move and it emitted a low hiss as its systems rebooted. At a frenzy he danced around the console hitting switches and pulling levels like lightning, throwing in the occasional smack with a hammer for good measure.

Just as the Darlek's eye lit up and it started to move towards the Doctor, he hit a final switch. Before it could finish the word exterminate it was evicted from the Tardis in a large flash of light. Sighing, the mad man took a moments rest before realizing something was still wrong, the Tardis was still on fire and had begun shaking.

"No! No no no no no." he shouted turning a screen to look. The Tardis was falling towards the Medusa Cascade, this was not good, not good at all. Rapidly he returned to flicking various dials, switches, leavers and whatever he could before jumping back and giving the console a good kick.

He looked around in grim horror, the controls weren't working, the Tardis was in free fall and he was doomed. As the Tardis shook harder and harder, he closed his eyes and awaited his fate. Eventually there was a large crash and the Doctor was thrown around like a rag doll.

Once the ship was still the Doctor stood up and checked the screen again, it was blank. Looking around he realized everything was blank. Apart from a few safety lights, the Tardis was dead. Poor girl would need a long time to repair after this. Looking down and noticing he still existed, he made sure the Tardis was completely still and approached the doors. Fires still raged around him but that didn't matter right now. What mattered was that he existed. He was sure he had flown into the Cascade, and by all sense of laws of physics, existing is something he shouldn't be doing.

Opening the doors he was hit by a wall of grey, smoke being emitted from a large crater in the ground. So there was ground then, good. He took a couple of steps before falling over, he tried to stand back up but to his alarm realized his legs weren't obeying him. Next there was a pain in his chest, putting a hand there he came back with blood. Not good, really not good.

Looking down he saw the wrench embedded in his chest, right next to his two hearts. The last thing he remembered seeing was a dash of rainbow, before passing out and his body erupted into light.

Chapter 2

Six ponies sat around a table inside a great tree. Correction, five ponies sat around a table and a sixth was hiding underneath the table, the sound of loud snoring scaring her witless.

"Oh come on Fluttershy," came the voice of one of the ponies. She had rainbow mane and tail, and like the pony under the table, was a Pegasus. "What's there to be afraid of, he's only a little pony."

"B-b-but Rainbow Dash," the little yellow Pegasus replied. "He arrived on the same day the disappearances started. Um, well I think it's just too much of a coincidence."

"Granted it does seem suspicious," a purple unicorn said, "However he has been in bed all week. It is not likely he is involved, unless you're suggesting he can kidnap them in his dreams." The unicorn thought to herself for a moment, "Then again, those strange flashes of light and energy readings do unnerve me a bit."

"Twilight dear, is it the light that worries you? What about the strange dust that comes out of his mouth, I mean that's so tacky and last season." A white unicorn responded, flailing her hooves in the air in a tacky attempt at dramatization.

"Well Ah'm just glad ya found him when ya did, sounds like he was seriously injured. But, can y'all run by me again the bit about the box and him stumbling?" asked a orange pony wearing a Stetson.

"Well like I was saying," the Rainbow mare began. "I was napping on a cloud by the edge of town when this box came screaming out of the sky. It flew right past me, almost knocking me off my cloud and hit the ground with a large crash." She flicked her tail with indignation, obviously upset her nap had been ruined. "Anyway, I flew close to the box to see what it was when the pony stepped out, except he wasn't a pony. When he came out he was standing on his back two legs, like a giant, soft version of Spike. He looked all funny wearing a bow tie and a fez. As he stepped out he fell, well more collapsed, and lay still. I could see he was injured, but as I approached his body was emitted light." Rainbow recreated covering her eyes with her hooves.

"Eventually when I could see again, instead of a strange creature, a pony lay there. Whatever he was before I couldn't let one of our own go without aid. First, I wanted to check out his box, but the doors wouldn't open. I did give it a quick buck to see if it would do anything but it was like kicking metal. Not the flimsy wooden door it appeared. Then the box disappeared..."

"Disappeared?" Twilight interrupted her.

"That's what I said, there was a weird whooshing noise and then the machine disappeared. It happened slowly, one moment it was there and the next it wasn't. I can't think of any other way to describe it," Rainbow finished rather exactly.

"But how did that happen?" Twilight asked again, "That doesn't seem possible." .

"Don't ask me, Twilight, you're the egg head." Rainbow Replied.

"Ah don't think it matters how it happened, what matters is it happened." Applejack said.

With this said there came a sound from upstairs. Twilight turned to Rainbow, "I think you should go see if he is all right, after all you're the one who saved him." Rainbow looked briefly excited before returning to her normal nonchalance.

"It's only fitting he meets the coolest pony in Ponyville first."

Chapter 3 - Not Ginger?!

The Dalek stood in the spotlight, its red cocktail dress diffracting the light off the surface of many sequins. Such grace the Doctor had never seen before in a species designed from its very genetic code up to kill, but graceful the Dalek was. Soon the band began to play and a Cyberman, wearing the most expertly cut tuxedo, approached the lone Dalek.

"Would you do me the honour of having this dance?" The Cyberman asked in a tinny voice, nervously playing with the back of his helmet with one of his large steel gauntlets.

"The honor would be all mine!" replied the Dalek, its voice reverberating as it echoed around the chamber.

Soon the Doctor found himself clapping with applause and jumping up and down on the spot, hollering like a mad-man at the sight of such a graceful dance couple. As the pair continued to dance he soon realized that the dance looked familiar. Of course the Tango, the passionate dance of love.

The dance ended and the Doctor was hollering at the top of his voice, jumping up and down his weight was taken by the barrier separating the circle of seats . Sadly the particular section of barrier had apparently been neglected by the maintenance crew and soon it was shaking. The Doctor didn't notice, and when he was falling the only thought in his head was still that amazing, if strange Tango. He was still thinking of it when his head hit the floor.

-x-

The Doctor was alive, despite what had happened he was alive. There were two feelings which confirmed this; first his head was pounding like a drum, pain didn't exist if you were dead. At least that is what he assumed. The second, there was a strange tingling all over his body, as if he was infused with a dangerous energy that would explode out of him if he was still for even a single second.

Of course if a Human had that feeling they probably would explode, since that feeling would most likely be coming from a large amount of electricity flowing through their body. For a Time Lord that got that feeling however, it meant something differently entirely, it meant regeneration.

He slowly opened his eyes, a soft light drifting through the crack in the eyelids. Soft light was good, Time Lords were known to be extremely photosensitive soon after regeneration. Something about the photons messing with the massive quanta's of energy flowing through the brain.

The first thing the Doctor saw with his new eyes was rainbow hair, rainbow hair? He shot upright in bed, rainbow hair meant multiple colours; multiple colours meant maybe ginger. The Doctor loved where this was going. Sadly he failed to hear the "Hey!" as he shot out of bed, so he was disappointed when he looked at the hair on his head in a nearby mirror. Brown! Always brown, every single regeneration brown. 'Couldn't the universe throw me a different colour occasionally,' he thought to himself.

He was so distraught with having brown hair he completely missed all the other changes. He turned around and saw the source of his confusion, "You!" he screamed turning on Rainbow. "You have the audacity to wake me and then the gall to trick me into thinking I might have ginger hair. Shame on you" he chided the confused mare.

She was just floating in midair her mouth open when the strange pony spoke again. This time his features suddenly a lot calmer. "Oh well no harm done. Which way is the door?"

Still stunned it was all she could do to point with her hoof and say "there," indicating towards the stairs.

With a quick "thanks," the Doctor walked over to the steps before pausing mid step at the top of the case. "Wait a minute..." her rushed back over to where Rainbow was still floating. "You're a pony?" she nodded, "and you can speak?"

The sudden, somewhat insulting question broke her out of trance, "Well duh. What do you expect? Not as if I'm a rabbit or swamp toad. Besides of course I can speak, I mean you can speak can't you?"

"I am not a pon..." the Doctor began to say before falling quiet, he remembered something else about his reflection that had seemed a bit off. "No no no no no no," he said as he rushed over to the mirror. "But that's impossible, I can't be equine, I can't. Time Lords are humanoids, always have been."

"Time what?" Rainbow asked. "Look, buddy, you must've hit your head pretty badly, you're a pony, not a Time whatever you said."

The Doctor looked at the mare, backing away he muttered himself, "This is not possible."

Rainbow giggled at the craziness of the scene, the pony must have really hit his head, however her eyes widened when she saw what was about to happen. "Look out," she cried, but it was too late. The Doctor tripped and fell down the stairs that he had been backing towards.

Chapter 4 -

Chapter 4 -

The Doctor was sitting on a sofa surrounded by six ponies, one of them was the rainbow coloured mare from before, the other five who were also female were of multiple colours and species.

With a mug of tea between his hooves and a bandage on his head he sighed, "Nothing like a brew to help you cope with a problem. Probably why the British once ruled a third of the world." The other six ponies looked at him strangely.

A purple unicorn approached him, shaking her head and ignoring his last comment. "So you say you're some kind of Alien being that fell through some rift in your dimension and arrived in ours."

"Pretty much, except the rift exists in all universes and that when I arrived I suffered extreme damage to my body and required regeneration to survive."

The Unicorn snorted, it seemed all her friends were willing to let her deal with the mad-pony for now. "Ah yes, this regeneration. You expect us to believe, without empirical evidence, that you were once a bipedal creature and for some reason the regeneration turned you into a pony? In short you expect us to believe your an alien?"

The Doctor put down his tea and scratched his head with a hoof. "Well, to be honest yes. Never had someone need much evidence before. Then again I never need to explain I'm an alien outside of some strange situation where people's lives are in peril. Really easy to prove myself in those situations." He paused for a second, "Now I think about it, the universe is rather strange at making things like my Tardis catch fire right when I need it most. At least this universe seems kinder."

He noticed the six ponies share a certain gaze, a gaze he had seen many times, a gaze which meant 'well actually...'

"So I take it you guys have a problem as well, why do I never get a break. First I'm not ginger, and now I have to save more lives. So whats the problem?"

"Well, um, actually no one knows." This time it was a yellow Pegasus that replied. "Four ponies have gone missing, but um, well that's all anyone knows."

"By missing you mean?" the Doctor asked.

"She means that they haven't been seen in over a week, and these are ponies who wouldn't disappear without telling no pony." Said an orange mare wearing a cowboy hat.

The Doctors ears picked up at the last part. "Obvious disappearances you say? Hmm that is strange, mostly when people get kidnapped without any information they are unknowns. People no one would miss, makes it less obvious you see. But if you say they are people know then that means they need those people in particular but why..?"

A white unicorn approached, "It seems you have quite the experience at dealing with these kind of situations darling. But what do you mean by they?"

"Well isn't it obvious?" asked a Pink pony before the Doctor could reply, the white unicorn shook her head. "Well they are whoever took our friends. That is who you meant right Doctor?"

"Right you are," he Doctor confirmed before doing a double take, "How do you know my name?"

"Oh I know everypony's name Doctor," the pink pony said wiggling her eyebrows.

"No really, have we met before or something mrs...?"

"Names Pinkie Pie," she said, "and this Twilight Sparkle; Applejack; Rarity; Fluttershy; and Rainbow Dash. And about that other thing I can't say, as you would say, spoilers."

He looked bemused as he tried to make sense of this entire siuation, stuck in a new universe with a new body, and already encountering a near paradox. 'Lovely.'

"Ok lets see, so you have disappearances, anything else so far?" The other ponies shook their heads, "Ok so how long ago was the first disappearance?"

"Um, about 2 weeks ago." Fluttershy answered. The Doctor simply nodded.

"Doctor, that is your name right?" the pony now known to him as Twilight Sparkle asked, he nodded. "What are we going to do?"

He smiled, "I'll tell you what we are going to do, we are going to look around the homes of the people who have gone missing, and get to he bottom of this mystery." he exclaimed with a certain gleam in his eyes. "Oh and we are going to run, the only thing I can promise, it will involve running."

Chapter 5

I know lots of grammar errors, but I want to get it out there. Working on Soarin's Pie and Artemis at the moment.

They entered Hay Stack's house, light streaming through the layers of grime on the windows,there were cobwebs everywhere. This was the sixth house they had visited that day, like all the rest despite being vacant for a week or less it was filled with dirt and grime which should take years to build up, not days.

The Doctor was followed into the house by Rainbow, Pinkie and Twilight. Rarity had gone home after the first three houses showed little; Fluttershy had been to scared to even come to any; and Applejack had to go home after the last house to help at the farm. Still three ponies were good enough companions, for at least what seemed a dead end mystery.

He had just finished studying the bathroom and was leaving when Twilight pointed something out to him. "Doctor, there seems to be water in the bath." He turned and gave her a look which said I know. "But look Doctor," she continued, "It's clean." It was true, everything else in the house had been covered with grime, which according to his sonic screwdriver, was natural. Yet here was a tub of water, now cold, but was clean.

"Hmm strange, very strange. Good spot Flashlight." Pinkie and Rainbow giggled at this mistake at her name while Twilight growled.

"It's Twilight."

"That's what I said," he dismissed. "Now we need to know why this water is clean," he said and probed it with his screwdriver which he held between his teeth. It was tricky and he almost dropped it in the water. "Hmm, nothing out of the ordinary, just some soap and general pony dirt, he obviously had been using this when whatever happened; happened." Frowning he continued, "Still doesn't tell us why it's clean."

"What if they don't like water," Rainbow suggested, "I know I don't. I mean it's good for pranks but I hate baths." A light lit up behind the Doctor's eyes.

"Rainbow your a genius," he said, causing her to smile smugly. "Although I haven't forgotten you tricking me into thinking I have ginger hair this morning." Twilight looked at Rainbow as if to ask whats that about and Rainbow shrugged her shoulders, during this Pinkie was busy sneezing due to the dust and was spraying confetti everywhere.

"Right so we need to think of why they are afraid of water?" asked Twilight.

"Exactly," the Doctor replied, a sinister gleam in his eyes. "So anyone able to think of why whatever has been behind this hates, or at least stays away from water."

"Well the cakes say I can't put pastries in the sink since it will cause them damage," Pinkie said. Then glassy eyed continued, "It's not fair they keep going on about that, I only did it five times, and the last time was Gummy's fault.

Everyone, even the Doctor looked uncomfortable, "She always like that?" he asked.

"Oh yeh, we kinda tune her out," said Rainbow.

"Right... Anyway despite her run along sentence, our Pink friend has made a good point.."

"I did?" asked Pinkie.

"Yes you did, it is quite possible that water is dangerous too them, in which case it is safe to assume they are somewhere dry, really dry. Wouldn't be above ground, lots of water vapour not to mention the rain, I mean you can't really control the weather..."

"Actually Doctor you can, in Equestria the weather is controlled by the Pegasus, they choose when weather should take place and set it up." Twilight interrupted.

"So you say you can control the weather here?" he asked and the three ponies nodded. "Hmm ok, so things make slightly more sense now." He paused for a minute thinking deeply. "Two of the victims are Pegasi right? therefore we can assume that their ability to make it rain could make them a target, if whoever it is causing this hates water. The question we need to ask ourselves is, why the other four? I mean our assumption about water could be way off and all of them have something else linking them, but 2 Pegasus and 4 non Pegasus doesn't make a strong case."

They sat there thinking, neither one speaking until they could think of something that connects the victims. However, as they sat there, they began to hear a clicking noise. Soft at first, but getting louder with each second.

"Doctor..." began Twilight, "it seems we are not alone."

The Doctor looked behind them into the main part of the house and froze, "Stay very still guys, and do not turn to look, what ever you do do not look" He whispered. Rising slowly to his feet he pointed the sonic screwdriver into the doorway, activating it he slowly walked out leaving his three companions in the bathroom all alone. There was a loud bang and the three of them looked at each other.

"Do you think he's all right?" asked Pinkie.

"I'm sure he's ok." said Rainbow although there wasn't much assurance in her voice.