Doctor Whooves: The Regal Sisters

by Gherkin

Rating: everyone
Tags: Doctor Whooves, Other, Princess Luna, Adventure, Princess Celestia, Crossover, Main 6, My Little Pony: Friendship is Magic
Length: 11422

A stallion Applejack met as a filly comes crashing back into her life, with extraordinary results.

Applejack's life isn't exciting, harvesting apples from sunrise to sunset. But when a crazy stallion she met as a filly comes crashing back into her life, the farmpony is whisked away on an adventure dating back to the beginning of Equestria itself.

A sequel has been written, called Discord and Time.

Published 2012-01-12 02:50:26 UTC
Last updated 2012-05-08 05:44:56 UTC

Chapter 1: An Unearthly Stallion

They all say that waiting for your cutie-mark is the hardest part of a schoolfilly’s life, and for Applejack it was no exception. She could never get used to all the bullying and name-calling, even though it had been going on for months. Today’s round was just the icing on the cake. Applejack couldn’t hold it back anymore. She collapsed to the floor and wept, the countless months of schoolyard teasing taking their toll. My life is worthless, she thought grimly, I’m nothing but a useless old blank-flank.

Slowly, she picked herself up and began her walk home. Turning a corner onto Mane Street, she somehow felt compelled to take the longer route through Ponyville to get home. Her thoughts still drowned out by depression, the filly almost missed it. Out of the very corner of her eye, she had noticed something extraordinary.

Standing at the end of a dank and dirty alley was a large blue shed, with the words “Police Box” emblazoned above its double doors. Intrigued, she inspected further.

“Police Box...” she muttered to herself, her eyes transfixed upon the unusual structure, “What in the hay is a Police Box?” Hearing a loud moan behind her, Applejack quickly turned around to see a brown stallion, with a messy brown mane, clutching his chest. He looks like one of them fancy big city ponies, all dressed up in that suit of his, she thought to herself.

“Are you OK, mister?” Applejack nervously walked towards the stallion in pain. Upon hearing her voice, his pain seemed to subside a little. He opened his eyes to look at the filly in front of him.

“It’s OK,” he spoke with a soft accent as he pulled out a piece of paper from one of his pockets, “I’m Doctor, um, Timey Wimey, chief advisor to the mayor of Manehattan.”

Applejack glanced at the paper, a look of confusion adorning her face, “Why are you flashing a blank piece of paper in front of me?”

The strange doctor’s eyes grew wide as he put the paper back in his pocket quickly, “Well, you see, it’s because, well.... um...” he stuttered, before collapsing in a violent coughing fit.

Applejack rushed to his aid, “Doctor, I think you need to get to a hospital!”

“No, it’s alright,” he told her, recovering from the unexpected trauma, “Now listen to me,” he kneeled down to match her eye level, “What’s your name?”

“Um, Applejack,” she mumbled.

“Applejack. In a sec I’m going to step into that shed of mine.” He gestured towards the blue box, “I want you to keep your eyes on it; I promise you’ll see something amazing.” He grinned before looking down at his hooves, which had begun to glow, “Looks like my time’s almost up,” he muttered solemnly, before stepping inside.

For a few moments, there was nothing but silence. Applejack turned to leave, but she stopped she heard a soft grinding noise behind her. To her amazement, she saw the blue box begin to magically disappear. A few seconds later, it was gone, with nothing but a few trash cans in it's place. Her eyes still unable to process what just happened, a smile began to spread across Applejack’s face.

Boy, those Manehattan ponies sure have a lot of style, she thought to herself as she started her walk home again, It’d sure be nice to live a sophisticated life in the big city. In fact, come to think of it, don’t I have an Aunt and Uncle who live there? A brilliant idea formed inside her head.

“So long Ponyville!” Applejack exclaimed out loud, “I’m goin’ to Manehattan!”

Matt Smith

Ashleigh Ball

&

Tara Strong

in

DOCTOR WHOOVES

THE REGAL SISTERS

“See you tomorrow, Applejack!” Twilight called.

Phew, that sure was a hard day’s work! Applejack thought to herself as she waved goodbye to her friend. I think I need to hit the hay. She dragged her weary body slowly back to the farmhouse. Walking into the kitchen, she saw her brother and sister sitting at the table, quietly enjoying a dinner of hay and oats.

“Hey sis!” Apple Bloom called upon noticing her sister’s entrance, “Finished harvesting the east orchard?” Applejack yawned and nodded slowly, before sitting down to eat.

Big Macintosh looked up from his food, “Hey AJ, did Twilight tell ya anythin’ about some sorta meteor shower that’s s’posed to happen tonight?”

“Yeah, she mentioned somethin’. I think. Why’d ya ask?”

“Well, me and Apple Bloom were going to go out and watch for a bit later. I don’t s’pose you’d like to come?”

“No thanks, Big Mac. I’m beat,” she told him, finishing her food. Saying goodnight, she got up and made her way upstairs. Not soon after, she was settled down in bed, ready for a good night’s sleep.

The hours passed by as the element of honesty drifted off into the world of her dreams. Apart from the myriad of chirping crickets, Sweet Apple Acres was silent.

BANG!

Applejack jerked awake at the sudden noise. Was there an explosion? Had something been broken? Was it a meteor? Either way, she had to find out. Climbing out of bed, she picked up a torch and set out to the apple orchards to investigate.

The cold air struck her as soon as she stepped outside. Gritting her teeth, she switched on the torch and pushed forward into the maze of apple tress that stood before her. It wasn’t long before she noticed a bright light in the distance, along with the distinct and familiar smell of smoke.

“Oh, horseapples!”

She ran as fast as she could toward the source of the fire, hoping to salvage whatever she could find. She began to slow as she approached the source of the fire. There was a clearing up ahead. Tentatively, she crept through the last row of trees and finally saw what had caused the chaos.

In the middle of the clearing was a large, smoldering crater. Inching closer, Applejack realised that it wasn’t a meteorite that had crashed into her apple farm. Inside the crater, much to her disbelief, was a blue box. The very same blue box that she had seen disappear in front of her eyes all those years ago. Even stranger, it was in pristine condition; even after falling from the heavens themselves there wasn’t even a splinter on the polished blue wood.

How could this be? Applejack’s mind could not process what had happened. The very same police box that disappeared magically falls from the sky, and there isn’t even a scratch?

How the hay does a box disappear and fall from the sky anyway? she thought. This was breaking every single law of physics Twilight had ever explained to her. Wondering aloud if the same stallion she met as a filly was inside, she trotted closer to the crater. As if on cue, the doors on the box burst open. A slight wave of fear suddenly gripped the farmpony as she backed away.

There was definitely something inside the box, Applejack could hear somepony grunting. It got louder, and louder, until, finally, a familiar looking stallion climbed out and fell to the ground.

It was definitely the same pony. He had the same colour scheme and cutie mark, even wearing the same suit. Yet, somehow, he looked younger. His face and mane had changed too. Where once was a scruffy, unkempt mess of hair now grew a long flowing mane. He doubled over in a violent coughing fit, succumbing to some unknown sickness.

Trying to relieve the mysterious stallion of his pain, Applejack caught him as he fell to the ground. He opened his eyes as she laid him down gently.

“It’s you!” he coughed and chuckled, “You were a little filly five minutes ago. Ha, what a coincidence!” Flashing a quick smile, he fell unconscious.

Applejack’s feeling of fear quickly turned to panic. She felt the stallion’s tense body relax and saw his cheerful smile replaced by a blank face, showing no signs of life at all. She felt for a pulse. He definitely had one, but it was erratic, unlike anything she had seen before. She was about to carry him back to the farmhouse when she noticed him open his mouth and release a vapour of gold dust into the air

“What the hay?” She stared in awe, mouth agape, as the dust floated away slowly into the atmosphere. Whatever kind of magic this was, it sure was creepy.

Heaving him onto her back, Applejack staggered back to her room at the farmhouse. The long walk back gave her time to reflect upon the night’s unusual happenings. However the more she thought about it, the less sense it made. She was expecting to wake up in her bed safe and sound any second now. The farm pony glanced at the snoring colt on her back, who was out like a light. Smiling gently, she continued her journey home.

***

No sooner had the roosters crowed had Applejack set off with her apple cart towards the town square. 'Timey Wimey', if he was indeed the same pony, hadn’t stirred once during the night, so she decided it was best to lock her room and go about her day as usual. As for the blazing crater and blue box in the middle of the apple orchard, she just prayed to Celestia that Big Mac didn’t have to do any applebucking today.

She reached the town square early. Only a few ponies were setting up their stalls for the day’s market. Taking her mind off the night’s mysteries, she opened her cart. She had just finished setting up when she heard a familiar voice calling out to her.

“Good morning, Applejack!” Twilight Sparkle greeted her friend with a happy smile. “Getting ready to sell some apples bright and early, I see!”

Applejack chuckled nervously. “Yep! Just setting up the stall, nothing strange goin’ on here! No sirree!”

Twilight eyed her friend suspiciously. “Are you sure? You seem kind of stirred up, are you OK?”

The farmpony chuckled again. “Me? I’m fine Twilight. There’s nothing unusual goin’ on at all!”

“So you call a meteorite landing in your apple fields last night nothing unusual?”

Applejack gulped. She knew she was beat. It was silly of her to think that Twilight hadn’t been star gazing last night. Leaning in closer to the unicorn, she whispered, “Alright, something real strange happened, OK? After the market, I need you to come back to my place.”

Twilight stepped back. “What do you mean? What happened last night?”

“I can’t explain it, OK?” Applejack snapped. Twilight recoiled slightly. “Just meet me here later.” The purple mare nodded in agreement.

Applejack sighed. “Now if you’ll excuse me, I got some apples to se-” she trailed off mid-sentence. Confused, Twilight followed her gaze to see a certain pink pony bouncing towards a young stallion trotting into the town.

“On second thought Twi, I think I might be needing your help right now.”

The unicorn giggled, still watching Pinkie introduce herself to the colt. “With what? It’s just Pinkie Pie being, well, Pinkie Pie.” she turned to see her friend gallop past her, sprinting towards the party pony.

“The Doctor?” Applejack heard Pinkie say, “That’s a funny name! Doctor who?”

“Just The Doctor,” the stallion told her, a little taken back with her exuberance, “Or sometimes ‘Spaceman’, or ‘Get off this planet’. Loads of people call me that.”

Pinkie giggled. “You’re funny, Doctor!” She noticed Applejack running towards her. “Hey, why don’t you say hello to Applejack, Mr. Doctor?” she suggested, beaming at him.

The Doctor turned to face the orange pony, who was glaring at Pinkie Pie. “Applejack!” he exclaimed. She raised her hoof to say something, but was cut off. “Now, I apologise for crashing my TARDIS into your apple fields but I had just regenerated and I wasn’t quite sure of my new body. Look, I got new ears!” He started flopping his ears across his face. Pinkie giggled and joined him. “So if you’ll just tell me where I can get something to eat, I’ll be on my way.”

“I, uh...” There were a million questions running through Applejack’s head. “Head on over to Sugarcube Corner,” she managed to say.

“Come on, I’ll show you the way!” Pinkie beamed happily, bouncing up and down.

“What was that about?” Twilight asked, watching Pinkie and the mysterious colt trot down the street.

Applejack shook herself out of her confused daze. “I’m not sure, but one thing’s for certain: that sure is one crazy stallion.”

“I’ll say,” Twilight replied, noticing them both shake their tails in the air, “Where’d he come from?”

“Sorry Twi, but it’s a long story.”

“I’ve got time.” She wasn’t going to take no for an answer.

“If I told you, you wouldn’t believe me.” Applejack told her, “Just meet me here later, and see for yourself, OK?”

***

The sun had almost set by the time AJ had packed up her cart. The town square emptied as stalls began to pack up and close down for the day. Searching the crowd, she and Twilight noticed The Doctor, now dressed up in a brown tweed jacket, complete with bow tie. Giggling to themselves, they started to follow him.

It looks like he’s going back to that blue box, Applejack thought, Whatever’s in there sure must be valuable to him...

It didn’t take them long to reach the clearing in the orchard. Strangely, the box was now standing next to the crater, still in pristine condition. Maybe Big Mac had pulled it out. AJ hoped he didn’t have too many questions. What was she to say? 'Oh, sorry Mac, a box just fell out the sky and ruined our orchards, it's no big deal.' She'd be committed for sure.

Snapping out of her thoughts, she saw The Doctor reach into his pocket and pull out a glowing key, which presumably opened the door. He grinned and shoved it into the lock, turning it excitedly. Hearing it click, he yanked open the door and galloped inside. Applejack was about to follow him when her friend stopped her.

“Don’t you think it’s a bit... unsafe to be following some crazy stallion you just met into a tiny blue box?” Twilight warned.

“I know it seems suspicious Twilight, but there’s just something about this thing.” She stared at it looming above her. “And I can’t put my hoof on it.”

There was an air of tension as she tentatively knocked on the door. She wasn’t just going to barge in unannounced; who knows what could be in there?

Before she could regret the decision, the door swung open to reveal The Doctor’s grinning face. “Hello!” he exclaimed, startling her, “Have you been following me?" He sighed, "First it's a pair of teachers, now it's a pair of ponies. What next?" He trotted back inside. "Come on in, there’s been a bit of a redecoration!” He stepped back inside. Wondering if following him had been a good idea after all, Applejack cautiously followed.

“Well, I’ll be...”

It was impossible. The whole box was impossible. Gazing around the large, bright room that stood before her, AJ no longer wondered how the Police Box had disappeared all those years ago, for it was abundantly clear. As for The Doctor, Applejack was sure that he was no ordinary stallion. Nopony in Equestria could perform this kind of magic, not even Princess Celestia. Noticing her amazed expression, The Doctor chuckled. “Any passing remarks, Miss Applejack?”

Lost for words, she just stood there for a moment. “You... you left a huge darn hole in my apple fields!” She replied angrily.

The Doctor looked up from the circular console in the middle of the glowing room. “Ah, sorry about that. To be fair though, it was a crash landing...” he trailed off, noticing Twilight by the door, her face identical to that of her friend’s.

“Applejack, what the...”

Before AJ could reply, The Doctor bounded in front of her, “Hello! I’m The Doctor, welcome to my TARDIS! Now, who might you be?”

Taken aback by the stallion’s enthusiastic greeting, Twilight managed to stutter her name before stumbling back in shock.

The Doctor smiled. “Yeah, she tends to have that effect on people. Or ponies, for that matter.” He frowned and muttered something to himself.

Overcoming her bewilderment, Applejack approached The Doctor. “OK, ‘Doctor’, what the hay is this contraption of yours?”

He turned to face her. “It’s my TARDIS. Stands for Time And Relative Dimensions In Space,” he explained simply.

“Uh, ‘scuse me?”

The Doctor sighed. “It’s a time machine. It can go anywhere, anywhen.”

“Ha! Yeah, right!” Twilight scoffed from across the room. “Alright, so maybe this thing is dimensionally transcendental, but the mere notion that it can travel through time is preposterous!”

“Is that so?” The Doctor smirked. “Alright then, Miss Sparkle, if you could go to any period of time, which one would it be?”

“Um, the first few years of Equestria?” she replied, confused by his question.

“Alright then! The early years of Equestria!” He turned towards the two mares. “Geronimo!” He yanked a lever on the console, causing the whole room to shake violently. Sparks flew from the console as The Doctor laughed manically, giddy as a schoolcolt. After a few minutes, the shaking seemed to subside. The ordeal was over.

AJ picked herself up off the floor. “What in the world just happened, Doc?”

He pointed towards the door, still beaming. “Take a look outside, see for yourself!”

Cautiously, she crept towards the door and opened it, stepping outside. Closing it behind her, she turned around to find herself face-to-face with an old, bearded stallion.

“Uh... howdy!”

Chapter 2: Can You Smell Gas?

The streets of Canterlot were eerily quiet tonight, lit only by the glow of the moon. Gazing up at it from his window, the young colt sighed. He turned back to the open casket that stood on the table before him. Memories of his mother rushed back to him.  He felt a silent tear trickle down his face.

“Farewell, Mother...” He closed the casket, sat down at his desk and started to write. The air was chilly, and the room had a terrible draft. Noticing the single gas lamp illuminating the room flicker and shut off, he got up. “Darn thing’s always going out,” he grumbled.

As he tried to light it again, a small gust of wing blew into his face. Seeing a dark liquid drip out of the lamp, he frowned. Great, he thought, Probably got nothing left in it now. Groaning, he lit a candle and returned to his desk.

*Tap*

That noise. It had come from the casket. Putting his quill down, the colt approached towards the casket and opened it. There was his mother, forever at peace. He was about to close it again when he noticed something. She was looking directly at him. He jumped back as she sat up and climbed out of the casket.

“Mother?” he said cautiously, “Is that you?” The undead mare advanced towards him. A cold wind suddenly blew through the room. Paralyzed with fear, the colt couldn’t move. He only cried in terror as his undead mother grabbed his neck. Struggling to escape her grip, the colt heard a large crack, and then nothing. His world turned to darkness.

Still standing in the middle of the room, the mare opened her mouth and screamed as a translucent blue entity rose through her mouth and shot back into the gas lamp. Another gust of wind blew through the room. The candle went out.

***

Being the element of honesty, Applejack never was too good at lying. So, when confronted by an old stallion because The Doctor’s box landed, of all places, inside his home, Applejack was literally lost for words.

“Well, who are you?” the stallion barked, “Tell me or I’ll alert the Royal Guard!”

The Doctor burst out of the TARDIS, flashing a piece of paper. “Commander Timey Wimey, commander of Manehattan’s guard, and this is Applejack, the plucky young mare who helps me out.”

“‘Plucky young mare’? Why you...”

The stallion stepped back a little, his anger fading away. “Excuse me, Commander. I apologise if I was a little forward. Allow me to introduce myself. I am...” he trailed off, noticing another mare exit the blue box.

Seeing the stallion before her, Twilight’s eyes widened and her jaw dropped in shock. “Star Swirl the Bearded!”

The old stallion stared at her as she started to jump up and down in excitement. “Yes, that would be me...”

Applejack rolled her eyes. “Here we go...”

“Star Swirl the Bearded is the father of the amniomorphic spell!” Twilight told The Doctor in response to his confused expression.

“Ah, well that would explain all the bowls...” he replied, noting the abundance of pottery around the room.

“Wait, what?”

“‘Amnio’ is Greek for bowl,” The Doctor explained, “So, effectively, our friend Star Swirl here is a ‘hairy potter’. Oh, I love this universe!” He chuckled and started to grin again.

Taken back by the ‘guests’, if you could call them that, in his library, Star Swirl went back to his potter’s wheel and began to work on an unfinished piece. “Well, yes, I am known for my pottery skills, I suppose.” The clay lit up as he began to mold it with his magic. “Now, Commander, I’m afraid I have to ask you to leave. It’s just that I have a very large order to fill from the shopkeep down the road.”

“Very well,” The Doctor replied, “We’ll just step into our box and be off then.”

“However, I am showcasing a few of my new spells at the local theatre tonight,” the bearded unicorn said, noticing Twilight’s disappointed expression, “It would be an honour if you could attend.”

Twilight’s face lit up. “Oh yes, that would be wonderful!” She trotted back into the TARDIS happily as it began to dematerialize. Not soon after, it had disappeared.

“Well, those fancy Manehatten ponies sure do travel in style.” Star Swirl muttered.

***

There was a chill in the winter air as ponies from all over Canterlot flocked to The Princess theatre to see what Star Swirl the Bearded had in store for them. Among them all were The Doctor and his two companions, happily cantering through the fresh layer of snow on the ground.

"So, Twilight," The Doctor said, a smug look on his face, "What do you think?"

The lavender unicorn was lost for words. "It's amazing Doctor!" she exclaimed, soaking up the different sights and sounds as they trotted through the snow, "I can't believe we're walking through Canterlot in the early years of Equestria! We even spoke to Star Swirl the Bearded! DO you know what kind of an honour that is?" She beamed at him.

The Doctor simply nodded, humouring her as they approached the theatre.

Not focusing on where she was going, Applejack bumped into a pale-faced mare. “‘Scuse me,” she said, dusting herself off. There was no reply. When she turned around, the mysterious mare was gone. Not paying too much thought to the incident, the trio trotted into the large auditorium, where the lights were dimmed. The performance was about to begin.

The curtain opened, revealing Star Swirl in his trademark outfit, a warm smile on his face. “Good evening, fillies and gentlecolts, and welcome to...” He trailed off, noticing something in the audience. As the audience turned to follow his gaze, they saw a pale mare, her face as white as the snow that covered the ground outside. Her mouth slowly opened, revealing three blue ghost-like creatures that quickly shot out into the air. Ponies screamed and fled as the monsters began to circle the auditorium.

“So, it’s you lot again, is it?” The Doctor seemed to call to them, “As if what happened back in Cardiff wasn’t enough! Don’t any of you have any original ideas?”

The ‘ghosts’ froze in mid-air, and turned to stare at the Time Lord. “You were not present during those events,” the leader growled. Its voice echoed though the air, as if there were more than one person speaking.

“I was actually. My face has changed a bit. Well, a bit more than my face really, but that’s beside the point.” The Doctor’s face bore a look of utter seriousness.

“Doctor, what are those things?” Twilight whispered.

“They’re a species called the Gelth,” he explained, “They lost their bodies in the Time War, so now they’re stuck in a gaseous state. I thought I’d beaten them, a long time ago, somewhere far, far away.”

Before Twilight could ask what the ‘Time War’ was, The Doctor was already addressing the Gelth again. “You know me. I’m The Doctor, and guess what?”

The Gelth glared at him.

“BYE!” Pulling a slim silver object from his pocket, The Doctor clicked a button. There was a sound of leaking gas as all the lamps went out, plunging the room into darkness. A gut-wrenching scream rang through the air. Upon instinct, Twilight used a spell to light the tip of her horn. To her surprise, the Gelth were gone.

“Where’d they go, Doc?” Applejack asked.

“I released all the gas from the lamps into the air, which forced the Gelth out of this poor lady’s body, and into the gas line.”

Twilight stared in awe. “Doctor, that’s brilliant!”

A smile appeared on his face. “I know.” Turning his attention to the pale mare lying on the ground, he clicked another button on the slim device, which he called a ‘sonic screwdriver’, and scanned her limp body.

“Is she alright?” Applejack asked him, fearing the worst.

“She’s dead,” he replied grimly, “But the somewhat-good news is that she died before the Gelth used her, because that’s what they do. Find a dead body and use it as their puppet.” He spat the last word out, disgusted by the thought.

“Uh, Doctor?” Twilight piped up.

“But we’re in trouble now, because we have no idea where they could be.” The Doctor continued, wrapped up in his thoughts.

“Doctor,” Twilight repeated.

“If I were a gaseous monster, where would I hide? Well, in the gas lines, I suppose...” He continued to ramble.

“DOCTOR!” the unicorn yelled. The Doctor jumped back.

“Uh, yes, Miss Sparkle?”

“We’re not the only ones here, you know.” She gestured towards the stage, where Star Swirl the Bearded still stood, mortified by the events he had just witnessed.

“Wh- wha?” The bearded unicorn managed to stutter.

“Oh look, it’s our good friend Star Swirl the Bearded!” The Doctor exclaimed, “Did you see how the Gelth crashed your performance like that? Why, the nerve of some people these days!”

“Commander-”

“No, it’s just The Doctor, I’m not really the Commander of Manehattan’s guard.” Star Swirl stared at him. “You actually believed me?” The Doctor chortled, “Well, there’s a first time for everything.”

“Doctor, then. What just happened?” Star Swirl’s eyes were still wide from shock.

“Extraterrestrial beings from another dimension just happened,” he replied, before adding, “Kind of like me.” He sat down on one of the seats. “Now, what are they planning...”

“Our numbers are few,” the leader’s voice spoke, seemingly out of nowhere, however The Doctor quickly deduced that they were communicating from the gas lines, via the lamps. “We cannot survive without the help of this planet.”

“Oh leave it out!” The Doctor told them, “Don’t bother playing the same trick on me again. You’re going to get us to trust you then backstab us when we least expect it. Do you think I’ve forgotten what happened the last time we met?”

“Then we want only one thing Doctor,” it said, ignoring him, “And that is power.”

“Yeah, and Freddie Mercury wanted a bicycle race,” he replied sarcastically, “There’s one thing I’d like to know though. How exactly did you end up in this dimension? The accident that brought me here almost destroyed my TARDIS.”

“You were present during the events that led to our arrival here,” it responded flatly.

“Oh, so that’s where you went!” The Doctor chuckled again, before becoming deadly serious, “Now, here’s the deal. You stop whatever you’re doing right now, and I’ll take you to a far away planet where you can live in peace. Because whatever you’re up to, I’ll put a stop to it.”

“There will be no negotiations.” With that, the voice was gone. The Doctor turned to his companions. “They hung up on me,” he said to them, “That wasn’t very nice.”

***

It was past midnight by the time The Doctor and his friends arrived back at Star Swirl’s library, which, according to Twilight, was coincidentally the same library tower she used to live in before moving to Ponyville. Not bothering to sleep, they decided to try and figure out what the Gelth were planning. Well, The Doctor did anyway. Applejack and Twilight had other ideas.

“Alright mister.” Applejack challenged the time lord, “You’ve got some explaining to do. Start off, what the hay is the ‘Time War’?”

A look of sadness suddenly adorned The Doctor’s face. “Well, I might as well tell you everything, since you’re both here now.” He pulled up a chair and sat down, motioning for the others to do the same. “I’m a time lord,” he explained, “An alien species, to you at least, from another dimension, like the Gelth. Except I’m the last one left. Years ago, my people fought a war with a race known as the Daleks. In the end, both sides were completely wiped out, because of me.” Twilight put a hoof to her mouth in shock. “I had to end the war, otherwise it would have engulfed the entire universe.”

“Then, how did you get here, Doc?”

“3 years ago,” he told them, “I’d just saved a group of astronauts from dying on the planet Mars, when I fell through a crack in the hole of the universe, and I landed here. Just like that.” He went to click his fingers, before stopping himself. “But I can’t go back, the crack’s too fragile. If I go through it would destory both dimensions.”

There was a long, drawn-out silence as The Doctor’s three friends took in this information, gaining a new outlook on their unusual friend. If you told Applejack about 48 hours ago that she would be travelling through time and space with an alien from another universe, she would have called you crazy. But now, well, it was par for the course, she supposed.

Star Swirl was the first to pipe up, “Back to the issue at hand, Doctor, how are you going to stop those creatures?”

The Doctor turned to face him, staring him straight in the eye. “I don’t know yet, I’ll think of something.” He turned to face the two mares. “I always do.” He flashed an eccentric grin.

“Hold up Doc,” Applejack said, “The Gelth said they wanted power, and I’m guessin’ they want a lot of it.” She replayed their conversation with the creatures from earlier on in her head. “How are they gonna try and get it?”

The time lord pondered this for a moment. “That is a VERY good question, and one that is in dire need of answering. To answer you though, I don’t know.” He stood up turned to the aged pony sitting beneath him. “Star Swirl, you’re the only one here native to this time period, you give us some ideas.”

Ignoring what The Doctor had mentioned about his time period, Star Swirl started to think. There were only two ponies in the whole world that had the power the Gelth wanted. His eye grew wide at the realization. “Dear sweet Celestia...”

“What is it?” The Doctor asked urgently, before hearing Twilight gasp in shock. “What is it Twilight? Somepony fill me in here!”

“The two most powerful ponies in the entire world are the two regal pony sisters!” Twilight exclaimed, sick with worry, “Doctor, if the Gelth get to Princess Celestia and Luna, what will that mean for the future? Last time I checked, my teacher wasn’t a zombie!”

“Time is in flux, history can be changed.” He explained offhandedly. “But if the Gelth get the Princess’, I’m guessing they don’t plan to rule peacefully for the next one thousand years.”

“What are we gonna do Doc? We don’t even know where these things are!”

“It’s simple really,” he said, with a look on his face that said ‘look at me, I’m being very clever’, “They can’t inhabit Celestia or Luna and harness their power unless they’re dead, so the first thing they’re going to do is...”

“Inhabit a dead body to kill them off first.” Applejack put two and two together.

“Exactly!” The Doctor told her, before turning to Star Swirl again. “What’s the closest funeral parlour, graveyard, or place with dead bodies in it to the castle?”

The unicorn thought for a second. “It would be Mr. Stone’s funeral parlour, in Mane Square!” He trotted towards his bedroom.

"Aren't you coming, Star Swirl?" Twilight asked him.

"I was already tired before my performance. To have it interrupted by inter-dimensional beings was, let's say, draining." He smiled slightly. "Besides, you both have your hooves already full with him." Twilight giggled.

The Doctor clapped his hooves together. “Alright then!” He turned to look at his companions. “Who you gonna call?” They stared at him, confusion appearing across their faces. The Doctor face-hoofed and whispered to himself, “Oh, right, I’m the only living thing in this universe that will ever get that.”

Chapter 3: Bow Ties Are Cool

The princess of the night looked down upon the streets of Canterlot, pondering over many things. News had just reached her of some sort of strange disturbance in a theatre in the center of town, however she and her sister had deemed it unimportant. Now, basking in the glow of her moon, she began to think about how she and her sister were going to rule for the next thousand years.

There was a knock on the door. Princess Luna turned around to see her older sister, having let herself in. “Hello, sister,” Luna greeted the sun goddess, who had a worried expression on her face, “May I ask, what is troubling thou?”

Celestia smiled slightly at her sister’s choice of words. “It’s nothing, really,” she answered quickly. Luna’s eye’s narrowed. There was no pointing in lying to her; somehow she always knew when something was wrong. “I’m being troubled by some nightmares I’ve been having lately,” she admitted.

Luna smiled warmly, putting a hoof around her sibling. “Do not be troubled by your dreams, sister, for they exist only within your mind.” She tapped Celestia’s forehead.

“It’s different, Luna,” the older princess explained, “They’re more like visions, visions of you.  Something to do with black magic, I-” she choked on the last word, tears streaming down her face.

Princess Luna hugged her older sister in a tight embrace. “You have nothing to fear, big sister. I’m not going anywhere.” She smiled gently.

“There’s something else too,” Celestia said gravely, “Something is coming, very soon.”

Luna let go of her. “What does thou mean?”

“A storm is coming, Luna. An oncoming storm.”

***

“I have one question. What in the whole wide world of Equestria are you wearing?”

The Doctor glanced back towards Twilight, who was walking through the early morning snow that covered the High Street. “Really, Twilight? We’re on a quest to prevent gas monsters from another universe brutally murdering your two princesses, and you’re questioning my choice of wardrobe? Get your priorities right!”

“But they’re so tacky! Where’d you get them from?”

“I bumped into Rarity, a friend of yours, I believe. She insisted that I get some decent clothes,” he answered simply.

Twilight struggled to contain a laugh. “Please! Rarity would never recommend something like that to anypony!”

“Well she didn’t, I chose it myself.”

“Yeah, it shows,” Applejack interjected, “What in the world possessed you to choose a bow tie?”

“Bow ties are cool!” The Time Lord defended, “Now, how far away is this funeral parlour?”

Twilight giggled. “Talking to yourself now, I see.” As if on cue, an ear-shattering scream echoed from a nearby building.

“Never a dull moment, huh?” The Doctor remarked before breaking out into a sprint, galloping around the corner. Sighing, Twilight and her friend followed close behind. The cold early morning air cut into the purple unicorn as she sprinted across the pitch black square. SO much for a peaceful trip back in time, she thought. Reaching the funeral parlour, The Doctor bucked in the door and leapt inside, brandishing his psychic paper to anyone who might have been paying attention.

Finally catching up, Twilight burst inside the barely lit parlour to see a ghostly pale body lying on the floor, stone dead. Standing above the deceased stallion was a mortified young filly backed against the wall, her terrified face stained with tears. The Doctor pocketed the psychic paper and moved closer to her, kneeling down to her eye level. “Hello,” he said in a soothing voice, “I’m The Doctor, what’s your name?”

“Lily,” she sniffed, “Lily Petal.”

The Doctor smiled warmly. “That’s a wonderful name. Where are your mummy and daddy Lily?” At that moment, a burly stallion burst into the room.

“Lily!” he exclaimed, embracing his daughter, “Oh, thanks Celestia you’re OK!”

“What happened?” The Doctor asked.

Lily’s father stood up to face him. “I have a better question. What are you three doing in my house, with my daughter?”

“We heard somepony scream, and came to see what was wrong,” Applejack told him simply, supporting her friend as she caught her breath.

“I heard something when I was in bed,” Lily piped up, “I came down to look and saw poor Mr. Quill just standing there. Then this blue thing came out of his mouth and flew through the window.”

The Doctor whipped out his sonic screwdriver and scanned the lifeless body. “Looks like they didn’t want to use Mr. Quill for their dirty deeds then.” He turned to Lily’s father. “I’d say they’re getting picky. What do you think, mister...”

“Tomb Stone,” he responded, oblivious as to what the crazy stallion was talking about.

“Of course it is,” The Doctor mumbled under his breath, before turning back to his companions. “They’re up to something,” he told them, “There isn’t anypony to inhabit between here and the castle, which means they’re making a different play.”

“Then what are we supposed to do, Doctor?” Applejack asked him, concern in her voice.

The Doctor stared her straight in the eye, a deadly serious look on his face. “We need to get to the castle, now.” Barging through them, he galloped out of the door. Applejack followed him, leaving Twilight to explain to the confused father gawping at her.

“Believe me, even I don’t understand him sometimes.” She quickly ran out the door. Tomb Stone shook the bewildered look off his face and embraced his daughter.

“So what’s the plan?” Twilight called, finally catching up to The Doctor.

“I don’t know!” he called back, a manic smile across his face, “I’ll figure something out!”

Great, Twilight thought, He really is crazy. She’d only been here a matter of hours, and already she was on a quest to stop the whole of history being re-written. No pressure at all, then, she thought. By now they had reached the long, winding stairs that led up to the castle gate. She slowed down to catch a breath, but, much to her chagrin, The Doctor galloped up them undeterred. Groaning, she followed him.

“Where are all the guards?” The Doctor wondered aloud, looking around the deserted courtyard, "I didn't even see any as we walked here. Even the Italian guards back in the Renaissance weren't this lazy."

“Princess Celestia won’t have night guards around here for at least the next five hundred years,” Twilight explained, still gasping for breath. “They all go home after sundown,” she added.

The three of them stared up at the imposing, omnious door that stood before them. Twilight didn’t understand why it made her so fearful now; she had always been in and out of the castle when she lived in Canterlot. Now, however, it felt spooky, as if it sealed some unknown evil inside. Gulping, she strode forward, before being stopped by Applejack.

“Hold on, sugarcube,” she warned, “This whole situation smells kinda fishy.” She glanced over at The Doctor, who was gazing at the door, deep in thought. “You’re the expert here, Doc. What’s in there?”

“The only ponies in the castle at this time are the two princesses and a few butlers,” he told them, trotting closer to the door, “No dead bodies though, that’s the key.” He paused. "Well, at least, there shouldn't be." He tentatively edged the door open, peering inside. The foyer was brightly lit by many different lamps. Multiple points of entry, he thought. It’s never simple, is it? The four of them crept inside. Twilight immediately set off on a brisk canter, heading towards the main staircase.

“Twilight!” The Doctor hissed, “What are you doing?”

“I’ve got to find Princess Celestia,” she whispered back, "I can’t let anything happen to her!”

“Princess Celestia isn’t going to meet you for another thousand years, Twilight,” Applejack pointed out, “We can’t just rush in. Who knows what’ll happen?”

“Applejack’s right.” The Doctor pulled out his psychic paper. “Luckily, you have me to rely on.” He flashed a cheesy grin, before trotting up the stairs.

“Wait! Didn’t you just say not to...” Twilight sighed. “Never mind.” They both trailed close behind. Taking in her surroundings, Twilight noticed that there wasn’t much difference between the castle she saw now and the one she would become accustomed to a thousand years later. She recognized paintings on the wall, even stopping to admire a certain portrait she had enjoyed looking at as a filly.

“Come on!” Applejack called, “Nothing’s gonna slow this one down.” She turned back to The Doctor, who had already turned a corner and disappeared from view.

“Sorry,” Twilight smiled sheepishly, “Had a bit of a nostalgia trip back there.”

They tip-toed down the corridor. The whole castle was like a dense maze of criss-crossing walkways and corridors, and it was easy to get lost. Losing The Doctor was the last thing they needed right now. They were about to follow him around the corner when they heard an elderly voice.

“Excuse me, sir. May I ask, what are you doing roaming the castle at this hour?”

Applejack peeked round the corner to see an elderly butler, traditionally outfitted in a tail coat and bow tie, speaking with The Doctor.

“I’m The Doctor.” She heard him say, “I’m here with my friends to see Princess Celestia. It’s pretty important, so you wouldn’t want to keep us waiting, would you? I doubt Her Majesty will be pleased with that.” The two mares edged around the corner and caught up with him.

The old stallion cleared his throat and straightened a little. “No, of course not.”

The Doctor smiled. “Thank you.” Stepping past the butler, the three of them continued down the corridor. “Nice bow tie, by the way,” The Doctor called out to him, grinning.

“Why, thank you sir,” the butler replied, before noticing a few of the gas lamps flicker. The Doctor stopped dead.

“Was it just me, it did those lamps just flicker on and off?”

“Don’t worry sir, they’re always on the fritz.” The butler went to inspect one of them.

“Don’t go near it,” The Doctor warned, but to no avail. What appeared to be a cloud of blue smoke burst out of the lamp. Inhaling it, the butler coughed.

“What the...” The butler doubled over in a violent coughing fit, thrashing around, before dropping to his knees and groaning in pain. Frozen by fear, the three of them could only watch as another entity seemed to possess the aged pony, turning his face icy pale.

“The Gelth...” Twilight muttered, “I though the could only possess dead bodies, Doctor!”

“They must have evolved.” The sudden realisation struck him. “This whole thing, it’s been a trick.”

“So what are we gonna do, Doc?” Applejack said worriedly, as the now undead butler advanced towards them.

“Well, when I say run, we, uh, run.”

"Oh, brilliant plan," Applejack snarked.

"Simplicity works best sometimes," he said, still backing away from the elderly stallion.

The butler continued to walk slowly towards them, not taking his eyes off The Doctor for a second.

“Shall we run now?” Twilight began to panic.

“It’s as good a time as any!” The three of them turned around and galloped for their lives. Running in no particular direction, Applejack noticed a large pair of double doors and decided to burst through them, the other two closely in tow. Tripping over her own hooves in panic, the farmpony tumbled over onto the floor, taking The Doctor and Twilight with her.

“Ugh, horseapples,” she muttered, before looking up. What met her eyes were the stunned faces of none other than Princess Celestia and Luna.

“Sister, remind me again why we don’t employ guards at night?” Luna whispered in her older sister’s ear.

The Doctor stood up quickly, shaking himself off. “Princesses! How coincidental! Right, no time to explain, there’s some inter-dimensional aliens about to make an attempt on your lives.”

The possessed butler slowly entered the room, the same blank expression on his face. “Alright then, you lot!” The Doctor called, “Where are the rest of you?”

“I am the only one,” the butler replied, his voice horrifically distorted.

“What happened to the others in the theatre?” The Doctor stood defensively in front of Celestia and Luna. “There were three of you.”

“Your sonic device managed to kill them, for they were still weak.”

“Then what’s the point?” The Doctor edged a bit closer towards him, “There’s only one of you now. Please don’t tell me you think you still have a chance with this!”

“Our plan was never to attack this land’s rulers.” The usual blank expression turned into an evil smirk, “But to attack you, Doctor, for what happened on Earth.”

“Oh that's great. Another psychotic revenge plot. Change the record, please. You can’t get in here.” The Doctor tapped his forehead, smiling smugly, “People have tried, believe me.”

“We don’t plan to attack your mind, time lord. We’re going to attack your heart.” The butler collapsed suddenly.

Princess Celestia pushed forward past The Doctor, kneeling down next to the dead stallion. Solemnly, she shut his eyes and rose to face The Doctor. “I knew something like this would be coming.” She sighed. “It was foolish of me to think that this was the only populated planet in our universe.”

“Well, you might be. I don’t know, but what I do know is that they are from another universe,” The Doctor told her, “and I also know that they’re still here somewhere.”

“Doctor, they said they were going to attack your heart,” Twilight said, “What did they mean by that?”

The Doctor though for a moment. “Well, the obviously don’t mean it literally, otherwise they’d have used a plural.” He put a hoof to his chin. “I don’t know. Really, I don’t.” He looked at the princesses, who were still shocked from the experience. “Applejack, what do you think?” He turned around. His eyes widened and his face lost colour.

“Oh no...”

Chapter 4: It's Better To Travel Alone

Over nine hundred years of traveling through time and space, and he still didn’t know any better. It was better for him to travel alone, because this kind of thing always happened. Every single time. Anyone who had ever traveled with him either ended up dead, or worse.

“Applejack!” Twilight’s voice snapped The Doctor out of his thoughts. The orange mare was unconscious on the floor, her body convulsing violently. Her friend rushed to her side, trying to talk to her, but to no avail.

“Get back, Twilight,” The Doctor said calmly, pulling her away.

She struggled to break free from his grip. “No, Doctor, I can’t just leave her!” Tears were pouring from her eyes.

“Leave it to me.” He knelt down in front of Applejack, gently placing his front hooves on her head. Immediately her body ceased seizing, and became still.

“Is she-” Twilight choked.

“She’s just unconscious,” Princess Celestia whispered to her, equally intrigued in the scene unfolding before them. They all looked back to The Doctor. He had a look of pure concentration on his face.

Putting his forehead to hers, he started to whisper. “Applejack, I know you can hear me.” Her face was glistening with sweat, “Fight it, OK?” His brow furrowed further, “I know you’re a fighter, don’t give up.” He remained still for a few moments, before suddenly jumping back, clutching his ears in pain. “No, no, NO!” He kicked the air in frustration. “Damn high pitched noises! I was so close!”

“What did you just do?” Twilight stood there, bewildered.

“Standard level telepathy,” he answered, “I can do it without magic.” Despite the grimness of the situation, there was still a tone of smugness in his voice.

“What happened?” Princess Luna, who had remained frozen in fear throughout the strange ordeal, suddenly spoke up.

“The Gelth, they blocked me out.” The time lord slumped over, thinking hard. “They can’t control her until they can take over her mind. Applejack’s fighting them, subconsciously of course, but I fear it’s a losing battle.”

“Then what can we do?” Twilight asked, holding back tears.

“I don’t know!” The Doctor groaned in frustration, “I just don’t know.” He hung in head in shame, a single tear managing to trickle down his face.

The silence was unbearable. After a few moments, Celestia’s face lit up. She turned to Twilight. “You are Applejack’s friend, I assume?”

“Of course, Princess, you know I am-” The Doctor glared at her. “Oh, right, another thousand years yet.”

“Then could you not use a memory spell, to help her remember all the wonderful times she has spent with you?”

“Wouldn’t work,” The Doctor spoke up, solemnly, “No matter what the memory, Twilight’s memory spell is still only standard level telepathy. He was quiet for a second. “But...” he got up to his feet, “Both of us combined...” He looked at them, a hopeful look on his face. “Oh, that’s BRILLIANT!”

The three of them looked at him, dumbfounded. “Well, what is it, Doctor?” Twilight said.

“Alone, our respective telepathic abilities aren’t enough to get through to Applejack,” The Doctor explained, “But if we could find a way to combine them...”

“Then we can get through to her!” Twilight finished, “Doctor, that just might work!”

The Doctor clapped his hooves together. “Right, here’s the plan.” He motioned for Twilight to come closer, “I need you to project the happiest thoughts of you and all of your friends into Applejack, via me.”

“So basically, you’re the messenger?”

“Exactly, except our telepathy combined is enough to break the Gelth’s hold over her.” He turned to the two princesses, “Oh, by the way, sorry about this. Hope we didn’t interrupt you, or anything.”

Twilight took a deep breath. “Are you ready?”

He nodded. “Geronimo.” With a wink, he knelt down, putting his hooves around her head again. After a few seconds, he whispered, “I’ve established a link.” Twilight nodded. She knelt next to him, her horn beginning to glow.

Gently, she rested her horn against his forehead. There was a slight buzzing as The Doctor saw all of the unicorn’s memories flash before his eyes. Playing with her big brother, enrolling in Celestia's School for Gifted Unicorns, moving to Ponyville, making her new friends. He studied all of her memories, before one particular scene began to play. Something that must mean something to her, he thought.

The orange mare struggled violently beneath her as Twilight gently lowered her horn. Their heads connected, and, slowly but surely, the mare’s bright coat began to regain its colour. Releasing her grip, the unicorn let Applejack stand up. She was dazed and confused. She looked around for a moment.

“Wh-what happened? Twilight!” Applejack shook her head, remembering. She sighed, and looked at her friend. “I saw vision of us feudin’ and fightin’. I couldn’t face the truth, so I started tellin’ lies.” She removed her hat and placed it at her chest, as if she was trying to hide behind it. “Can ya ever forgive me?”

Twilight smiled warmly. “I already have.” Applejack smiled back.

The scene faded to black. The Doctor smiled. “Come on Applejack, you’re doing great.” After a moment, he released his grip, and stood up.

“Did it work?” Princess Luna asked, genuine concern on her face.

The Doctor and Twilight looked at each other, grinning. “Oh, it worked alright. Right now, our good friend Applejack is just sleeping. She’ll wake up soon.” He told them.

“But what about those creatures?” Princess Celestia approached him. “The Gelth, you called them.”

“Gone,” he answered simply. “See, when they control someone, living or dead, they become just an entity. Like a bad memory, easily erased. Which, to put a long story short, is what we just did.”

***

"Wh-what happened?" After about an hour, Applejack came to, much to the delight of her friends.

Twilight smiled. "It's a long story."

"The Gelth invaded your mind, we stopped them, now they're gone," The Doctor explained simply. Twilight glared at him. "What?" He turned away, whispering to himself, "It wasn't that long."

“Wait.” Princess Celestia stopped them as they were walking out, “You never explained to us, who exactly are you three?”

The Doctor chuckled. “Oh, you’ll find out, in about a millennium.” They smiled at the look on her face. “Give or take.” They went to leave when he stopped. “You know what? I don’t fancy walking, and I think you two deserve something to make up for us interrupting your evening.”

“Well, what?” Luna asked bluntly.

The Doctor pulled out his sonic screwdriver. “Oh trust me, it’s something really cool.” He pressed the button. The device whirred for a moment, before silence. Suddenly, a large gust of wind blew through the room, and, seemingly out of nowhere, a large blue box began to appear in the center of the room. The grin temporarily disappeared from his face when he looked the slim device in his hooves, which was partially destroyed, it’s blue tip cracked.

“Hmm, must have shorted it out. It was getting old anyway.” He chucked the device away. “Ah well, she'll give me a new one.” He leant against the box.

The two princesses stood there, amazed. “What is it?” Celestia managed to say.

“This,” The Doctor told them, opening the door, “Is my TARDIS.” The three of them stepped inside. Soon after, the middle of the room was empty again.

“Well,” Luna murmured, “That was unexpected.”

1000 years later...

Pinkie Pie bounced happily down Ponyville Mane Street. It was a beautiful day; the sun was shining, birds were singing, and the party pony was happy as can be. She loved meeting new ponies, and the funny stallion she had met the previous day was one of the funniest ponies she had met in a long time.

In the distance, she heard a strange grinding noise. Huh, that was kinda weird, she thought, before starting to bounce down the street again. All of a sudden, something bumped into her, knocking her to the ground. Looking up, she was surprised to see Twilight and Applejack with the funny Doctor standing over her.

“Pinkie!” The purple mare tackled her in a tight embrace. “Oh, I missed you all so much!”

“But we saw each other yesterday!” Pinkie freed herself from Twilight’s grip. “Where have you been?”

Applejack chuckled. “It’s a long story, sugarcube.” She too embraced her friend.

Pinkie smiled, before looking over the farmpony’s shoulder. “Hey! Doctor! Where do you think you’re going?”

The Doctor, who had been making his way back to his blue box hiding away in an alley, froze in his tracks. “Well, I-um, well…”

“You’re not going anywhere!” She said, a sudden assertiveness to her voice, “Before I throw you a party!”

The Doctor laughed nervously. “Well, I’m flattered that you would throw a party just for me, but I really need to-“

“Don’t be silly! I throw parties for everypony new in Ponyville!” She grabbed his tail, dragging him towards Sugarcube Corner to make preparations.

***

The party was impressive; a true testament to Pinkie Pie’s party-throwing skills. The Doctor, at first hesitant to the idea of being the center of attention of the whole town, soon warmed to all the friendly ponies greeting him. Rainbow Dash, however, was suspicious of the town’s new guest.

“So what exactly are you a doctor of, anyway?”

“Everything, my dear Rainbow.”

“You can’t be a doctor of everything, that’s not possible!”

He sighed. “Let’s just say it’s my special talent, OK?”

Rainbow paused for a second. “Then where does the hourglass come in?”

“I’d explain it to you, but you’d probably get confused.”

She smirked. “Try me.”

“Do you know anything about the rules of inter-dimensional travel?”

She stared at him for a second. “Alright, you got me.’’ She flew off in a huff.

He smiled, before glancing around the room. Almost everyone in town was here. I’ve seen some parties in my day, he thought, but nothing as big as this. And all for me! I should feel honoured. He noticed the white unicorn that he had gotten his outfit from across the room. What was her name? Rarity, that’s the one. She was with a rather timid looking yellow pegasus.

“Doctor!” She called out to him. The look on her face suddenly changed. “You’re still wearing the bow tie?”

He gave her an offended look. “It’s cool, and you know it. Besides, who’s your friend here?” The pegasus glanced up at him quickly before backing away, trying to hide behind her long, pink mane.

“This is Fluttershy,” she told him, before whispering in his ear, “She’s a bit shy.”

No, really? He thought, before smiling again. “Hello, Fluttershy. I am The Doctor.” He extended a hoof. She took it awkwardly, shaking it before returning to her ‘hiding place’.

“I take it you’re one for all things nature, Fluttershy?” He said, trying to make conversation.

“Oh yes,” she said, suddenly becoming more sociable, “I love everything about nature! It all just fascinates me!”

“That’s nice. I guess you could say I’m sort of into the whole ‘nature’ thing myself.”

She gasped. “You are? We have so much to talk about!” The most adorable smile appeared on her face. “We’re going to be the best of friends!”

“Maybe,” he told her as she led him to a quieter part of the room.

***

The rest of the night was a blast. The time lord had gotten to know each of Twilight’s friends a little better, and got into some sort of conversation with almost everypony in town, even if it was just a brief introduction. Even a grey pegasus with a strange pair of eyes was a joy to speak to, even if she did sound and act a bit clumsy.

The night was drawing to a close. Most of the ponies in town had left or were too tipsy to notice him leave quietly. He had managed to slip out of the room unnoticed before being stopped by Twilight and her five friends.

“Doctor, please don’t go, just as we’re getting to know you.”

He motioned for her and Applejack to come closer. “You saw how dangerous it was back there. Applejack, you were almost killed.”

“Can’t y’all at least stick around for a while?”

He sighed. “I’m sorry, I really am. But wherever I go, trouble seems to follow. Too many people I’ve known have had their lives ruined because of me.” He closed his eyes. “I can’t let anything happen to any of you.” He walked away, leaving them both stunned, and owing an explanation to the rest of their friends.

He soon located his machine. He took a moment to admire it, not quite knowing why. Passing his hoof along the polished wood, he pulled out the key, opened the door, and stepped inside. Slowly making his way around the center console, he pulled on a lever, smiling slightly at the noise he had become accustomed to over the years. He looked at the readings on the monitor. His jaw dropped.

“What.”

He read the Gallifreyan on the screen, double and triple checking it to make sure it was correct.

“I can go back…” he whispered to himself, “Back to Earth, to my universe…”

Before he could think any more on the matter, the console made a beeping noise, and a brand new screwdriver popped out. “Ah, a new one!” He picked it up, deciding to test it on an old radio that happened to be lying around. He clicked the button, but nothing happened. The device just beeped and did nothing.

“What? Don’t tell me you sold me a faulty product!” He extended it, revealing a set of six lights, none of which were illuminated. The lights each had a distinct colour: purple, orange, blue, white, pink, and yellow. He studied them for a moment, before a smile grew across his face. “Oh, you clever thing!” He yanked a bunch of levers, making the whole room shake.

“Hold on Ponyville, I’m coming!” he shouted, before laughing manically. "Geronimo!”

Epilogue

After what felt like forever, the shaking finally stopped, and the TARDIS became silent. The Doctor had landed. Bursting through the door, he took in his surroundings. It was mid-morning, and the TARDIS’ readings told him that it was about a week after his party. He was also right next to Rarity’s boutique, however, strangely, there was nopony to be seen.

“Where is everyone?” he thought aloud. In the distance, he could hear music, and a familiar voice singing a catchy tune. “Pinkie!” He galloped towards the center of town. As he drew closer, he began to make out the lyrics of her song.

“It makes me happy when you beam, beam, beam, yes it always makes my day…”

The Doctor finally reached Mane Street, where there seemed to be some sort of parade following Pinkie Pie, who was now being lifted up by all of her friends. I guess they really like their musical numbers around here, he thought, before taking after her, calling out her name.

“Come on everypony, smile, smile, smile,

Fill my heart up with sunshine, sunshine,

All I really need’s a smile, smile, smile,

From these happy friends of mine!”

He managed to catch up to the singing pony, who noticed him as the crowd behind them kept singing. “Doctor, you came back!” She grabbed him and hoisted him up next to her, being carried along by the rest of her friends. Before he protest or say anything, she wrapped her hooves around him in a tight hug. “Please don’t go anywhere this time,” she whispered into his ear.

“I promise.” He smiled at her. Smiling back, she grabbed his bow tie playfully and leapt off her friends, the confused time lord in tow. They landed in the middle of the town square, a large crowd of happy ponies surrounding them. Letting go of him, she began to belt out a finale.

“Yes, a perfect gift for me,

It’s a smile as wide as a mile,

To make me happy as can be!”

As she sung the final lines of her song, The Doctor couldn’t help but feel overwhelmed by the sense of happiness and joy that was all around him. Whipping out his new sonic screwdriver, he saw that all six lights were brightly lit. He looked around at the spectacle before him, before putting a hoof to his face, feeling a single tear roll down it. He chuckled slightly. “How…” he struggled to find a word, “Equestrian.”

Pinkie had finished her song by that time. She bounded up to him, her friends close behind.

“So,” Applejack said, “Are y’all stayin’ for good this time?”

He tapped his chin in mock thought. “Well, I could, or you could all travel with me for a while, if that’s OK with you.”

“Where would we travel to?” Rainbow Dash asked, uncertain.

Twilight smirked. “Trust me Rainbow, anywhere you like.” She giggled at her confusion. “Why don’t you show the rest of us, Doctor?”

He smiled. “It would be my pleasure.”

***

“It’s just a big, tacky blue box!”

The Doctor sighed. Should have known she'd be like this. “Rarity, is there anything about me that doesn’t offend you in some way?”

She thought for a moment. “Well, I think your mane is rather dashing.”

He looked her in the eye, smiling slightly. “Thank you.”

Rainbow Dash tapped him on the shoulder. “How are we all gonna fit in there? Heck, I’m surprised you fit in there by yourself!”

“Well, you would think that, wouldn’t you, Dash? Don’t worry, I can change that.” He clapped his hooves twice. The doors swung inward, revealing the impossible room that lay within. Intrigued, the six of them trotted inside, leaving the time lord alone outside the boutique.  Hearing all the astonished gasps coming from inside, he grinned, before stepping through the threshold and closing the doors.

For a moment, there was nothing but silence. However, after a few moments, the magical machine began to fade out of existence. Next stop: everything.

***

Princess Celestia stared out of the window of her castle in Canterlot, watching the sun rise over the mountain that the royal city stood upon. Taking a sip of her tea, she turned her attention to the pile of letters on her table. She picked up the first on the pile. Yet another letter of negotiation from the Griffon Kingdom. Putting it aside, she was about to read the next one when she saw her sister in the doorway, accompanied by a royal guard.

"Your Majesty," the guard said, saluting.

"Commander." She nodded in return. "Forgive me if I sound forward, but, what are you doing here?"

"A stallion gave this to me, said it was to be delivered to you personally." He held out a dark blue envelope, sealed with the shape of an hourglass.

Celestia smiled. "Thank you, Commander. You may leave us now."

The guard left the room. Once the door had closed, she looked at her sister. She was thinking the same thing. Winking at her, she opened the envelope and began to read.

***

167 days down, Celestia knows how many days left to go. The spirit of chaos looked around the Canterlot Royal Gardens. Heck, it was about the only thing he could do during his eternal stone imprisonment. That and counting the days that had gone by since he had been defeated by the Elements of Harmony.

Princess Celestia underestimated him. What she didn’t realize was, if he focused enough, Discord could sense strange happenings and disturbances throughout the universe, and right now, there was one doozie of a disturbance. There was some sort of a crack in the fabric of the universe. This was good news.

The crack was creating enough chaos in the fabric of reality to create an escape route, albeit a small one. If he could just focus enough and find somewhere close enough to the crack to escape to. To his delight, an impossible blue box was spinning through space nearby. Focusing his energy, Discord managed to morph into the console of the machine.

Looking back, he saw that his body was still in Equestria, encased in stone. Guess I’ll just have to do with my mind, for now at least. Looking around the large room surrounding the console, his gaze fell upon six familiar ponies. He smiled. Fate, luck, coincidence, call it what you want, but Discord was just about to get his rematch with the Elements of Harmony.

Sequel

Hey all!

The sequel to this story is up, and can be found here!

Doctor Whooves: Discord and Time

Have a nice day!

-Gherkin8088