Doctor Who, My Little Pony 1. The Mad Colt with a Box

The Emotional Illness

Chapter 1: The Mad Colt with a Box

Had you, on that day, simply looked down at Ponyville from the rolling hills around it, you would have seen a quaint Equestrian town, complete with a library housed in a hollowed-out tree, a stage used for the inhabitants' numerous celebrations, and several outlying apple orchards dotting the countryside. Had you only glanced, you would have noticed nothing wrong.

But if you were to let your gaze linger on that point in the valley, you would have felt an uncomfortable feeling, a sense that something was amiss, and despite your better intentions, you would have desired to steer clear of that town as you made your way through the valley.

But even that strange observation would tell you nothing of the town's true situation, of the darkness that hid within.

* * *

><p>The streets of Ponyville were bare, neither pony nor beast daring to use them. The morning was devoid of the cheerful chatter between friends and neighbors, or the <em>clip-clop<em> of hooves as they walked, worked and played. The air, usually filled with the aroma of fresh pastries from the kitchens and bakeries, was stale, unpenetrated even by nature.

The night had given way to a beautiful sunrise. But there was nopony outside to enjoy it.

The Ponyville library was the only building in obvious use. It was here that Twilight Sparkle had made her residence, and where she was now worriedly tearing through her bookshelves.

"No, no, no…" She opened book after book with her magic, flipping through the pages, hoping that there was something, anything she had overlooked the last time. But once again, her efforts yielded nothing.

She sighed as she began to replace the mountain of books that had accumulated during her search. Normally, Spike would have assisted her, but he was among the numerous victims of the town's crisis.

After finishing her task, she stepped out of her adopted home. Even now, the utter lack of activity in the town surprised her, deepening her mood further.

Applejack walked down the road, pulling along a cart full of food and supplies gathered from various houses. "Mornin', Twilight," she greeted, her normally bright tone replaced with fatigue. "Can ah get you anything?"

"No, thanks, AJ," Twilight said, dipping her head appreciatively. "I'm going for a walk if anyone needs me."

"Alright. Y'all be careful now, ya hear?"

The sound of Applejack's cart faded slowly as Twilight continued down the dirt road, and she found herself missing it. It had served as a reminder of the town as it had been, and hopefully would be again.

The sights of the valley did little to lighten Twilight's mood. How could they, knowing the horrors contained in Ponyville? Even she, having been there, could hardly believe what was happening. In the span of a month, the entire village had become unrecognizable. She felt her mood couldn't improve even if Celestia herself descended from Canterlot and embraced her then and there.

She was so lost in her thoughts that she didn't notice the box until she ran into it.

The blue box was a curious thing to behold, not just because of its unusual location, but also because it was unlike anything Twilight had seen before. It was identical on all sides but one, where double doors presumably opened to whatever was inside. A sign was posted on the right door, detailing something about police that Twilight did not understand. A cylindrical object adorned the top, which the mare presumed was a light. It was off, but another light was visible through the box's opaque glass windows. Though she wasn't sure why, Twilight got a strange impression that the box was both old and new at once, that it both had been placed here just moments ago and had been here forever. Curiosity overcame her as she reached towards the door handle.

It was then that a colt burst his head out the door with a cheery, "Hello!"

Twilight jumped back in fright. "Wha – who are you?"

The colt stepped out of the box and subsequently tripped over his own hooves, landing face-first in the grass.

Twilight slowly walked closer to him. He was a light brown earth pony with a complementary dark brown mane. His cutie mark was an hourglass shape, making her wonder what his special talent was. Unlike most ponies, who found little use for clothes outside of special occasions, he wore a blue suit with a red tie. Twilight wondered what exactly he was doing in the box, dressed so well.

"Um…are you okay?" she asked, leaning over him.

"Sorry, sorry about that," the colt replied, shakily getting up. "I'm still getting used to these. I mean, _hooves!_ Nothing like a new set of feet to show you how much you take your toes for granted. Especially pinkie toes, I miss those little guys."

He looked up from his rambling to see the purple mare staring at him confusedly. "Oh, sorry!" he said, taking her hoof and shaking it firmly. "Hello, I'm the Doctor. And you are?"

"Twilight Sparkle," she replied.

"Right, Twilight." The Doctor fidgeted for a few seconds, looking around randomly before finally saying, "Sorry, bit of an idiot, but…where am I?"

"Well, Ponyville's just a few minutes down the road," Twilight replied, motioning behind her, "but you probably don't want to go there right now. The entire town's caught a weird sickness."

"A sickness, you say?" the Doctor said, intrigued. "That's good – well, it's bad, really, but it's good because I am…" he paused as he reached into his suit's pocket and pulled out a card and waved it in front of Twilight's face. "Doctor Whooves, pony doctor extraordinaire. But it's just 'the Doctor' to you."

The card was flashed too quickly for Twilight to see the details, but what she saw looked very professional to her. "So, you're here to help us?" she asked excitedly.

"Yes, indeed," he affirmed before running down the road. "Well, there's no time to lose. Come on, Twilight! Allons-y!"

"He had run about thirty feet before Twilight said, "Uh, Doctor? Ponyville's this way."

The colt looked down the path both ways before turning around and breaking into a run again. "Yes, of course! Let's go, Twilight! Can't keep those ponies waiting!"

The mare shook her head in bewilderment and took off after the strange colt who called himself the Doctor.


	2. All the Strange, Strange Ponies

**Chapter 2: All the Strange, Strange Ponies**

"So, Twilight, tell me about this sickness."

The two had slowed down to a walk after the Doctor had tripped over himself numerous times during his mad dash towards Ponyville. His balance was steadily improving, but Twilight was still amazed by his clumsiness.

"Well, it all started about a month ago," she began. "A few ponies started getting depressed suddenly and fell ill a few days later. It happened again the next day, and it soon spread over the next few weeks, until nearly every pony in Ponyville was sick. There are only six of us left healthy, and we've got our hands full."

"Yes, how did you manage that?" the Doctor asked. "Not getting sick, and all that?"

Twilight sighed. "I don't know. And honestly, I almost wish I _would_ get sick."

A nearby apple tree reminded Twilight that she hadn't eaten breakfast that morning. She plucked an apple with her magic and took a bite out of it. It didn't taste as sweet as normal; Applejack hadn't been able to tend the orchards for some time.

She stopped chewing when she noticed the Doctor staring at her.

"Do that again," he said.

The mare swallowed. "What?"

"The thing with the apple and the glowiness," he said, waving his hooves in an attempt to explain.

"You mean…this?" Twilight's horn glowed as she waved the apple through the air.

The Doctor's face broke out into a smile wider than Twilight thought possible. "Oh, that is _beautiful!_" he exclaimed, leaning towards Twilight to get a better look at her horn. "Biologically produced zero-point energy! Brilliant!"

Twilight stepped away from the strange colt. "Yeah…haven't you seen magic before?"

"Magic? Well, I don't know about that, but this is _amazing!_ Can all ponies do this?"

"Just unicorns," she replied confusedly. "Where have you been all your life? Everypony knows that."

"Oh, here and there." The Doctor said, shrugging. "Just not _here_, here. But I've never seen anything like – ah! We're there."

The Doctor ran towards Ponyville, leaving Twilight to wonder if Pinkie Pie had just met her match in randomness.

* * *

><p>"Ah, there ya are, Twilight," Applejack said as she heard hooves behind her. "I need some help with – ah!" She turned around to see two ponies instead of one. "Who's yer friend, here?"<p>

"Applejack, this is the Doctor," the purple mare explained. "He's here to help us with the sick ponies."

The colt grinned. "Yep, that's me. Doctor Whooves, certified pony physician." He whipped out his card the same way he had done with Twilight.

Applejack gave him a confused look. "That paper's blank."

The Doctor paused only for a moment before regaining his composure. "Oh, yes, yes, sorry!" he said quickly, looking at the card. "This must, er, be one of the blank ones. Oh, well, that's not important." He stuffed it back in his pocket and led the two mares further into town. "So, where do I start?"

"Uh…we're keeping everypony in the town hall," Applejack answered. "'Twas the only place big enough to hold 'em all, 'cept for the barn, but I think you'd understand why we didn't –"

"Applejack?" A new voice came from town hall. A white pony with a well-cared-for purple mane and tail stepped out of the door. "Have you seen Twilight? Spike's acting oddly around me again," Her eyes fell on the Doctor. "Oh, hello, sir!" she said cheerfully.

The colt returned her smile. "Hello, I'm the Doctor."

"Rarity, at your service," she replied, batting her eyelashes. "If there's anything you need, dear, and I mean _anything_, don't hesitate to ask."

"I'll be sure to. Now, the patients are in here?" he motioned to the building. "I hope it's not as bad a New New York. Well, technically, it was New New New New New New New New New New New New New New New York, but that's beside the point." He continued to ramble as he entered the building.

The three mares stared after him. "Well, you've certainly roped yerself an interestin' colt, haven't you, Twilight?" Applejack said, winking.

Twilight gave her a confused look. "What?"

"And my, isn't he a looker!" Rarity said. "A little rough around the edges, but still very dashing."

Twilight's cheeks began to redden. "I don't know what you're –"

Their conversation was interrupted by a loud thump. A quick look told them all they needed to know: the Doctor had met Pinkie Pie. The two had landed in the road, the Doctor on his back and Pinkie standing over him, hopping excitedly.

"Hi! I'm Pinkie Pie!" she said cheerfully. "What's your name? Where are you from? How'd you get here? What's your cutie mark? Can we be friends?"

The Doctor stared at her. "Uh…the Doctor, Gallifrey, TARDIS, hourglass…and, yes?"

"Yaaaaaayyy!" Pinkie jumped even higher than before. I'm so happy you're here! We haven't had anyone new in weeks because all the ponies are sick, and because all the ponies are sick, nobody wants to play, and everypony's _soooooo_ sad, but then I heard you talking outside and I was like –" she gasped dramatically, "NO WAY! And you walked in and I said 'Hi! I'm Pinkie Pie!' and I asked if we could be friends and now we're friends!"

The Doctor dusted himself off, wondering if he had been wrong to accept her friendship. "Yes, and you also tackled me doing so."

"Uh-huh!" the mare affirmed happily.

"Right…" the Doctor rubbed his brow. "Listen, it's been lovely meeting you, but I've got…doctor stuff to do, so, if you'll excuse me…" he edged past Pinkie Pie, and then ran as fast as his legs would carry him into the doorway before someone else had the chance to stop him.

"Wow!" Pinkie Pie beamed. "He's so noble, rushing off to care for his patients! I should throw him a hero party when he's cured everyone!"

Twilight shook her head as Pinkie hopped after the Doctor, not surprised that the colt had received a welcome from Pinkie Pie similar to her own.

Her amusement melted to depression when she saw the situation inside. The building was packed wall-to-wall with the residents of Ponyville, some of the ponies so ill that she couldn't look at them without feeling sick herself. Twilight's heart sank; how could one pony hope to fix all this?

The Doctor was undeterred, judging by his animated conversation with Rainbow Dash.

The blue Pegasus was eager to flaunt her abilities to somepony new. "Yeah, some say I'm the biggest, baddest, fastest pony in Ponyville," she said. "I don't like to brag, but, they're right! I've got moves that'll make your head spin!"

The Doctor, however, was more interested in her wings. "Amazing! And you can actually achieve flight with these?"

"Um, duh? Every Pegasus can." She flashed a cocky grin. "Just not as awesomely as me."

Twilight coughed. "That's all very nice, but don't you have a sickness to worry about, Doctor?"

"Ah, yes!" The colt ran to a bed and looked up and down the pony that occupied it. "I just need to get a good look before – oh, hello!"

A sudden, "Meep!" was heard as a cream-colored pony jumped up and hid behind a nearby desk.

"Oh, dear, you spooked the poor girl!" Rarity sighed. "Now she won't come out for ages."

The Doctor walked slowly towards the desk. "Hey, hey, it's alright," he said softly, kneeling closer to the frightened pony. "I'm the Doctor, what's your name?"

The young mare poked her head out slightly. "I-I'm…Fl-Fluttersh-shy…" she whispered.

"Fluttershy? That's a beautiful name," the colt said, smiling warmly. He edged closer, lowering his voice to match her whisper. "Listen, Fluttershy, I'm here to help you. I'm going to get these ponies better, so you can come out now, alright? Come on, it'll be okay."

She lowered her head bashfully and walked out from her hiding spot.

"See?" The Doctor said, gesturing her to keep coming out. "I'm not a bad pony. A little kooky, perhaps, but not bad."

Fluttershy giggled softly. "Thank you for coming to help us, Mr. Doctor."

"It's my pleasure. And please, it's just 'Doctor.'"

The mare nodded, blushing slightly, and ran to join her friends.

Twilight walked over to the Doctor as he began to examine the sick pony again. "I'm impressed, Doctor. Nopony's ever handled Fluttershy that well before."

"Well, you don't come away from all the places I've been without picking up a few things," he said digging in his pocket. "Like how to use Venusian aikido with only four limbs. Still haven't quite figured that one out yet, though." He pulled out a silver-colored stick with a blue tip. He pointed it at the pony and pressed a button; the tip lit up and made a whining noise. "But _blimey!_ All these ponies in a month? That's impossible. Well, it should be, anyway."

Rainbow Dash crossed her arms. "Great! A disease that shouldn't be happening, and all we have to help us is a doctor who refuses to make sense and whose only skill so far is to calm Fluttershy." She huffed in defeat. "We had better resources when we went to find the Elements of Harmony!"

The Doctor looked up from his work. "The Elements of what?"

"The Elements of Harmony," Twilight repeated. "You don't know? It's…kind of a long story."

The Doctor pulled up a chair and sat down facing its back and putting his arms on the headrest. "Well, we're not going anywhere, are we? Besides, I love a good story; it takes the edge off of life-and-death situations. Especially having the in-laws for tea."

* * *

><p>With constant interruptions from both the Doctor and the six mares, the story of the quest for the Elements of Harmony and the confrontation with Nightmare Moon lasted well into the afternoon. Most of the Doctor's questions were centered on magic – he was especially fascinated with Spike's method of letter delivery – and details about the manticore and the sea dragon. The others simply wanted to "correct" Twilight's narration with their preferred version of the story.<p>

The Doctor rubbed his chin thoughtfully. "So the Elements of Harmony are essentially vessels of psycho-empathic energy, and you six are the metaphysical embodiments of their power?"

The six mares all stared in silence; even Twilight was baffled by his terminology.

"I…guess?" she ventured.

"Brilliant!" the colt cried, jumping out of his seat. "I love new planets."

A moan brought their attention back to the sick ponies around them. The Doctor ran over to the colt, putting glasses on and pulling out the silver object again.

"His condition is worsening," he said, waving the object up and down in front of the colt, "but I'm not detecting any responses from his immune system. No white blood cells, no hemoglobin, nothing. But why?"

"None of our medicine is working, either," said Twilight. "They didn't have any effect on their bodies at all."

The Doctor's head snapped up. "No, of course not, because it's not a sickness of the body, it's a sickness of the _mind!_" He pointed the stick at the colt's head. "But what kind of neural disease causes an emotional response before a biological one? Think, Doctor, _think!_"

The silver rod beeped suddenly. He stared at it for second, eyes widening.

"Is that good?" Applejack asked.

"No…oh, no, that's very bad…" the colt said, turning to the mares. "And it's not just them…it's you, all of you…"

He started to run out of the building, but was caught by the tail by Applejack.

"Ah-ah-ah-owowOW!" the colt yelled, falling on his backside. "Blimey, was that really necessary?"

"Just hold yer applecart, Sugarcube." said Applejack. "You ain't just dashin' off an' leaving us in the dust with nary an idea what's goin' on."

"Well, then come along," he said, running out the door, "We have to get to the TARDIS!"

"The what?" Rainbow Dash asked.

"Just follow me, alright? We have no time to lose!"

Left no other option, the six mares took off after the colt, not knowing how much stranger their lives were going to get.


	3. The Ponies Have The Phone Box!

Chapter 3: The Ponies Have The Phone Box!

For the first time in a month, the sound of running hooves echoed across the valley as seven ponies ran down the dirt road. Nature took notice; birds looked down from their nests, bunnies poked out of their holes, and squirrels turned from their nut gathering to see them as the six mares chased after the blue-coated colt.

"Coshtarnit, Doctor!" Applejack yelled. "Can't ya slow down for one apple-pickin' second?"

Twilight didn't know what to make of the Doctor. Just this morning, he had been stumbling over his own hooves in the middle of the forest; now he had become a rambling colt who they were struggling to keep up with.

The Doctor finally slowed when the edge of the forest came into view. He led them farther in, stopping in the clearing where Twilight had first met him with the blue box.

"Right where I left her," he said, fumbling in his pocket.

Rainbow Dash wasn't impressed. "So, you led us running all the way out here, leaving all those ponies behind, just to show us a tiny blue shed?" Seriously, what kind of pony are you?"

"Well, technically," said the Doctor, "I'm not a pony. I'm a Time Lord, from Gallifrey. And this is not a shed, it's a –"

"Alright, that's it!" Twilight stomped her hooves. "I can take finding you in the middle of nowhere, stumbling over your own hooves, and your babbling about Celestia-knows-what, but now you claim you're not even a pony? Has anypony ever told you that you're _crazy?_"

"Once or twice," the Doctor admitted, pulling out a key and inserting it into the box's lock. "Well, more like ten times. Well, more like every person I've ever met. But you're the first pony, so good job on that."

Twilight slapped her forehead and groaned. "Oh, this is too much!"

"Alright, it's your choice if you don't believe me," the colt said, shrugging. "I'll just step inside my 'shed' then and leave you on your merry little way." He opened the door just wide enough to fit through and slipped in.

"Oh, no you don't!" Twilight yelled, following the colt into the box. "You're coming out and telling us who you…really…are…"

The box's interior was enough to silence any further accusations the mares held. It was impossibly large, rising higher than the trees outside and wider than their trunks. The walls were painted gold and dotted with white octagonal lights. In the center, a clear pillar rose, its base surrounded by a console covered with all kinds of instruments.

The Doctor leaned against the console, crossing his front legs with a confident grin. "So…what do you think?"

The mares simply gaped at the room until Pinkie Pie jumped up excited and shouted, "Oh! Oh! I know! It's bigger on the inside!"

The Doctor smiled even wider. "Even ponies say it. I love it!" He jumped up and beckoned them forward. "Go on, take a look around. Just be careful, and whatever you do, don't –"

"WOAH!" Rainbow Dash yelled from down the hallway. "There's even more stuff over here!"

Any control the Doctor had over the group was instantly lost as they ran through the halls, discovering what other wonders were in store.

"Oh, my!" Rarity gasped. "What a magnificent wardrobe! Such exotic designs and – what? _Bowties?_ Ugh! How dreadful. That simply will not do."

Applejack sniffed as a familiar scent caught her attention. "That smell…it can't be…an apple orchard! I don't believe it! There's sunlight an' ev'rything in here!"

"Aw, cool! He's got a pool in here!" Rainbow Dash said excitedly. "It's even got waterslides! This is so _awesome!_"

"Oh my gosh!" Twilight gasped. "This library is gigantic! All these books…I couldn't read all these in a hundred years!"

Pinkie Pie hopped from room to room, her attention continually stolen from one place by the next. "Oh, what's this? Hey, that looks cool! Ooh, shiny! I could have the biggest party EVER in here!"

The Doctor noticed that Fluttershy hadn't left the control room; rather, she seemed awestruck, perhaps a bit afraid, of the chamber's enormity.

"Like it?" the Doctor asked, wrapping his hoof around her shoulders as the other five ponies returned. "I call her the TARDIS – that's Time and Relative Dimensions in Space. I've travelled all around the universe in this girl. As you have seen, there are all kinds of rooms here, but this," he extended his other hoof and waved it in front of the console, "this is where the magic happens."

Pinkie Pie reached for a lever. "Oooh! What's this do?"

"DON'T!" the Doctor yelled, diving across the room to protect the lever in question from the hyperactive pony. "_That,_" he said slowly, "is the Wibbly Lever. I'm not quite sure what it does yet, but there's a slight chance it could tear a hole in time and space roughly the size of Belgium if not used correctly." He eyed the six mares. "So please, unless I ask, don't. Touch. _Anything._ Got that?"

The six mares all nodded in fear. After a few seconds of silence, the Doctor smiled and rubbed his hooves together. "Right-o! Twilight, I'm going to need you for some tests. Now, don't give me that look, this won't hurt a bit…"

* * *

><p>A few more-or-less painful minutes later, Twilight Sparkle stood covered from head to hoof with wires, instruments, and other strange objects she couldn't identify, all culminating with a metal dome that sat uncomfortably on her head. The wires led to the TARDIS' console, where the Doctor busily pressed buttons and turned knobs (with some difficulty, thanks to his new anatomy). The other five mares had taken seats around the room, having become bored of the Doctor's project some time ago.<p>

"I swear, I am never going to participate in any of your ideas ever again, Doctor," Twilight said bitterly. "If this doesn't kill me first."

"Oh, don't be like that," the Doctor said, while trying to figure out how on Gallifrey he was going to use the keyboard with hooves. "Think of this as a science experiment. Imagine: 'The Doctor and Twilight Sparkle: Discovering the Mysteries of the Ponyville Plague.' Hmm, 'Ponyville Plague,' I like that. Could somebody write that down?"

"What exactly is this theory of yours, Doctor?" Rarity asked.

"Hold on…" the colt tried to type, but soon threw up his hooves in frustration. He then pulled out his sonic screwdriver and, holding it between his teeth, used it to tap out a command.

"There we go!" he said as he finished. "Anyway, Rarity, it's not really a disease, strictly speaking; it's more of a series of symptoms caused by outside manipulation by a foreign entity."

"Smaller words, Doc," Dash said boredly.

The Doctor sighed. "Aliens are doing stuff."

Wires rattled against each other as Twilight moved towards him. "Okay, I'll admit I was wrong about this whole TARDIS thing, but…aliens? Really?"

"Of course, Twilight. I'm an alien, after all. Time Lord, remember?"

Twilight looked up and down at him in amazement. "But…you look pony."

"You look Time Lord," the Doctor countered, then looked up thoughtfully. "Actually, you don't; I do look pony right now, so I guess that makes me a Time Pony. Did we even have ponies on Gallifrey? Because, if we did, and they shared certain biological features with us, then technically they'd be Time Ponies, unless of course –"

"Doctor!" Applejack yelled.

"What? Oh, yes! Sorry!" He went back the main computer. "Where was I? Oh, yes – aliens are doing stuff."

"Alright," said Twilight, "assuming there are 'aliens doing stuff,' how do you know? You just wave your little blue flashlight and that proves it?"

"First of all, it's a sonic screwdriver. Second, yes, that's part of it."

"And the other part?"

The Doctor rotated the screen around for her to see. "There's one in you right now."

The six mares gasped as they saw the readings. Inside an outline of Twilight's body, a dark, amorphous blob writhed around. An unearthly noise, something between a hawk's screech and a bear's roar, emanated from the creature. As it moved, strange tendrils stretched towards Twilight's head and latched on to her skull.

"And it's not just her," the Doctor said in a serious tone, "there's one inside all of you, and everyone in Ponyville. That thing is a species of empathivore. The more common variety, the _m__ö__rk__ö__n_, has a physical form, but this one here is entirely composed of psychic energy."

Twilight slowly shook her head, eyes wide with fear. "No…it can't – that's impossible!"

"Anything's possible," the Doctor replied. "Little guys like that are wiggling inside your brains as we speak. As psychic energy, an empathivore can jump into a person's mind and generate a small field of despair, around itself, causing their host to feel negative emotions more readily. It then feeds off that energy, and uses it to grow and multiply, while the host slowly dies. After that, it's a simple matter of finding a new body to begin anew.

"What's curious about yours, though," he continued, leaning against the railing, "is that yours are entirely docile. No psychic leeching, no despair field, nothing. They're just…there."

"So how do we find out why?" Twilight asked.

"Research!" The Doctor jumped up and walked to the door. "We'll just pop back into Ponyville, do a few more tests on the sick ponies, and – oh."

The mares joined him and looked out the door to see every pony from Ponyville standing outside the TARDIS, all with no signs of sickness.

And with blood red eyes.

"Backinbackinbackin!" The Doctor pushed the mares backward and closed the doors just as the first ponies slammed into the TARDIS.

"What the heck was that?" Rainbow Dash demanded. "They were all bedridden when we left!"

"The empathivores can take over their host's bodies when threatened," the Doctor replied, running to the center console. "It's how they keep people from stopping them if they are found out!"

Dash rolled her eyes. "Well, that would have been nice to know a few hours ago. We could've locked them inside town hall!"

"I didn't think they had enough energy yet!" The colt ran around the circular panel, pushing and pulling on a seemingly random sequence of buttons, knobs, and what appeared to be a bike pump. "Besides, I don't think a wooden door would have stopped them."

"But that door's wood!"

"No, it just _looks_ like it!" As he pulled a final lever, the glass orb in the center column began to move and the whole room started to shake.

"What's happening?" Rarity asked.

"I'm starting up the TARDIS," the Doctor replied. "It's time we got to the bottom of this. Strap yourselves in, girls; we're going to Canterlot!"


	4. Shadow of the Past

**Chapter 4: Shadow of the Past**

The white walls of Canterlot gleamed in the midday sunlight. As Equestria's capital, the city displayed some of the finest architecture in the country, commissioned by Princess Celestia after the castle in the Everfree forest was abandoned.

With the return of Luna from exile, the Equestrian government had required some rearrangement to allow for the younger alicorn to rule alongside her sister. Most of the day, the two found themselves up to their necks in matters of state in some form or another, but at this moment, the two were sharing a rare moment together, appreciating the escape from schedule for what it was.

Unfortunately for them, the calm wasn't to last.

A loud rumbling filled the princesses' quarters. Celestia and Luna stood up, eyes looking for the source of the sudden noise. Their question was answered when a wooden blue box slowly faded into existence in front of them.

Luna shrank behind her older sister, afraid of what the box might bring. Celestia simply looked on in confusion.

The box's door opened, and a blue-suited brown colt stepped out. "And that," he said, seemingly to no one in particular, "my fine equestrian friends, is the only way to travel."

Applejack stumbled out of the box. "I'll stick to my own four hooves, thank ya kindly."

The princesses' confusion grew as the remaining five bearers of the Elements of Harmony all exited the box with similar discomfort (save for Pinkie Pie, who insisted that they all ride again), ending with the purple unicorn Celestia knew very well.

"Twilight Sparkle!" she gasped. "What is the meaning of this?"

"Princess Celestia!" the six mares quickly bowed. Twilight shot a glance at the colt. "You didn't say we were going to land _in her bedroom!_" she hissed.

"To be honest, I didn't know, either." The colt muttered, glancing back at the box they arrived in. "I wish she'd tell me these things more often. I almost think she enjoys these awkward situations."

The colt approached the dumbstruck princesses with a smile and kneeled. "You must be the Princesses Celestia and Luna. I'm the Doctor; very pleased to be in your audience –"

"Princess!" Three royal guardsponies burst into the room. "We heard noises and –" The leader caught sight of the seven ponies. "You! How did you get in here? Who –"

"Stand down, captain," Celestia said calmly. "These are my…" Her gaze lingered on the Doctor. "…friends. They are welcome."

The captain gave the Doctor a suspicious look before leaving with his subordinates.

"Now then," said Celestia, facing the group, "Perhaps you can explain your sudden appearance in my chambers, Twilight."

The purple unicorn mumbled several false starts before pointing at the Doctor and panicking. "It's all _his_ fault! It wasn't until he showed up that weird things started happening and all this stuff about aliens and Time Lords and boxes that can fly and – and – and –"

"Calm yourself, Twilight," The Sun Princess interrupted. "I'm not mad at you, just…perplexed."

Celestia walked towards the Doctor. "It seems my student believes you to be responsible for this, Doctor. Would you care to explain?"

"Certainly," the colt replied, moving so he stood between the six mares and the two princesses. "Now, I'm sure you are at least partially aware of the situation in Ponyville?"

Celestia nodded. "Twilight informed me of a sickness almost a month ago, but I haven't heard anything since."

"Well, then I think you should know that it has spiraled spectacularly out of control thanks to a bunch of mind-infesting things called empathivores."

Both of the princesses stiffened at his final word. The Doctor's gaze hardened. "But you would know all about them, wouldn't you?"

"What in the hay is that supposed to mean?" Applejack asked.

"Empathivores don't just come out of nowhere," the Doctor explained. "And they're an awful long way from home…" He focused his gaze on Luna. "…which means someone brought them here."

Celestia blocked her sister from the colt's view. "She didn't know! We thought they had been –"

"Sister."

Celestia stopped, surprised that her sister had spoken up. "I think…it would be best if I explained it to him." She looked at her hooves. "After all, this is partially my fault."

The Sun Princess hesitated, then dipped her head in agreement. Luna stepped forward, wary of the Doctor's gaze.

"Over a thousand years ago, I ruled over Equestria alongside my sister. It was a different, smaller kingdom back then, but we still ushered the sun and moon as we do now. It was a good life, but as I looked at our subjects, I began to resent my role. The ponies worked and played under her sun, but when the moon came into view, there wasn't a soul awake. The more I saw that pattern, the more I began to believe that Celestia was loved, and I was not.

"Naturally, I grew jealous of her, but for months, I never dared to admit it. I tried to ignore it, to simply do my duty as always, but those feeling never truly went away.

"But it all changed in one night. As I raised the moon, I felt something new in the night sky, an object unlike anything I had seen before. A ship made of metal, floating through space! I reached out to it, and found the creatures you call 'empathivores.' They had taken control of the vessel's original crew, but those bodies had long since died, leaving the ship adrift as I found it.

"As we conversed, they sensed my long-dormant jealousy, and saw an opportunity. They asked that they would be allowed to enter my mind, promising to help me get the respect I thought I deserved." The dark mare shuddered. "Like a foal, I agreed. They came into me, and immediately, I heard their thoughts among mine, whispering to the darkest parts of me to bring them out. I used my magic to become Nightmare Moon, and refused to lower the moon the next morning."

"So when you were Nightmare Moon, it was really the empathivores in control of your body?" Twilight asked.

"No." Luna said without hesitation. "I was in full control during the whole ordeal. They were a great influence, but I was still the one responsible for my actions.

"Anyway, you all know what happened next. Celestia immediately sensed the dark presence in my mind. The Elements of Harmony were her only weapon, but she could not use their full power – that was meant for chosen ponies such as yourselves. Using what power she could, she trapped me on the moon I once governed."

"A spell that would last one thousand years." The Doctor turned to Celestia and frowned. "One. Thousand. Years. What did you think would happen? The empathivores would die? Luna would break free of them? But no; they remained. They had Luna to feed on, and she had a lot of life and anger left in her. And she sat there, waiting those thousand years out, as those monsters chewed on the corners of her mind. She could have gone mad from that, Celestia. For all you knew, she could have died!"

"I know, Doctor," Celestia replied, looking at her sister. "And not a day has gone by since then that I wished I hadn't."

"Sister…" The two princesses nuzzled, Celestia wiping the tears from Luna's eyes.

"But what happened?" Rainbow Dash asked. "Obviously they didn't die; so why are they only showing up now?"

"When you defeated Nightmare Moon, you forced them out of Luna's body," the Doctor explained, "but you didn't kill them. They must have been weakened considerably, so they probably have been piggy-backing in some ponies' heads until they recovered; they were most likely the first to fall ill."

"And I gather by your presence that things have taken a turn for the worse?" Celestia asked.

The door was burst open by the same guards from before. "Celestia! My lady, there's a mob of ponies marching to the gates! Something's wrong with them – their eyes… they're all red!"

"I think that answers your question," said the Doctor.

* * *

><p>A full regiment of Celestia's royal guard lined up in front of the castle gates. Before them, the empathivore-controlled citizens of Ponyville marched towards them, almost daring the princesses to act first.<p>

Fluttershy shivered behind the Doctor. "Those poor ponies…w-will they do that to us too, Doctor?"

"Not if I can help it," the colt replied.

The cream-colored mare looked into the Doctor's eyes in amazement. "Aren't you afraid of…monsters?"

The Doctor winked at her. "No, Fluttershy; they're afraid of me."

He walked over to Celestia. "I need you to hold them off as long as you can."

"We will do what we can," Celestia replied, "but I refuse to hurt my little ponies."

"I don't expect you to," said the Doctor, walking away. "Come along, Twilight, Rarity, Applejack, Rainbow Dash, Fulttershy, Pinkie Pie. Blimey, that's a mouthful. You ponies need a team name or something."

"I can assume you have a plan, Doctor?" Celestia asked.

"Not yet; working on it!" he shouted over his shoulder.

The Doctor led the six mares down the hall and into a room. "Right, I need to go fetch the TARDIS. Don't go anywhere, I'll be right back."

He ran off down the hall. A few minutes later, the blue box reappeared in the room, and the Doctor emerged carrying a strange object.

"So, it took a generous disregard for conventional laws of physics and my best coffee maker, but I believe this will work." He placed the device on the floor. It was shaped like a tower, with small bits of metal sticking out like tree branches. The top pulsed a rainbow of colors and six helmets were attached to the base by cables.

"And just what in the hay is that s'posed to do?" Applejack asked.

"The reason why the empathivores didn't get to you," he explained while making adjustments of the device, "is because you six hold the Elements of Harmony. You need to generate energy to cover the whole planet to get them all."

"The whole planet?" cried Rainbow. "How do you expect us to do that?"

"That's where this baby comes in," the Doctor replied, patting the machine. "You six wear these helmets, and it will multiply the energy and release it in one big bang." He handed out the helmets to the six mares. "In theory, anyway."

"In theory?" Twilight asked incredulously.

The Doctor scratched the back of his head. "Well, I haven't actually seen the Elements in action, so all I had to go off of was the readings I took from you earlier and your descriptions of how it worked, so…" He trailed off as the mares looked at him fear in their eyes. "It'll work! I promise!" he affirmed with a smile.

Pinkie Pie narrowed her eyes at him. "Do you Pinkie Pie Swear?"

The colt raised an eyebrow. "Do I what?"

Pinkie moved until there was barely an inch between them. "Cross you heart, hope to fly, stick a cupcake in your eye?"

"Eh…yes?"

"Okie Dokie Lokie!" Pinkie smiled and bounced back to her helmet.

The sound of something colliding with the castle gates echoed across the room. The Doctor clapped and rubbed his hooves. "Alright, girls, we haven't got much time; let's get to work! Allons-y!"

* * *

><p>The guardsponies struggled to put their weight against the gates. The castle was not built to withstand a siege of any kind, as Equestria had not known war for over a thousand years. Though the guards were well-trained, their expertise lay in non-lethal combat; the empathivores were willing to use their pony hosts to kill if necessary.<p>

The captain of the royal guard made a hurried bow as he approached Celestia and Luna. "My ladies, we are doing what we can, but those…things won't let up. We can't hold the gate much longer."

Celestia nodded. "Reinforce the gate as much as you can, then fall back. We only need to keep them from the Elements and the Doctor."

The captain saluted and made his way back to the stallions under his command. Luna looked up at her older sister. "So much rides on that colt…do you think his plan will work in time?"

Celestia looked down the hall the colt had run down earlier, where he was doing something she couldn't discern. "I don't know," she answered, "but when I look at him, I get a feeling…that even though I just met him, I could trust him with anything."

Luna gave Celestia a small smile. "I know, sister. I get that feeling, too."

And so the Princesses of Day and Night joined the guards and watched the gate, waiting for the Doctor's plan to unfold.

* * *

><p>Though her eyes were closed, Twilight could practically see the Doctor pacing nervously around them. The sound of the gate collapsing and soldiers fighting in the hallway had given them all a sense of urgency and a worry that the machine was not working fast enough. The meter on the device was so very close, but it moved agonizingly slow. They were cutting this too close.<p>

A sudden shout came from the hall. The mares opened their eyes and saw four empathivore-controlled ponies had found them and were running towards them.

The Doctor stood between them; the determined look on his face told his intentions to all.

Twilight reached to stop him, but was too late. He charged the ponies, undoubtedly too aware that they could toss him like a rag doll.

A wave of emotion came over the six, and with it, the meter hit 100%.

The light from the machine glowed brighter than the sun as a rainbow of energy cascaded from it. It flew with such force that every pony in the castle was knocked off their feet. The wave continued wiping across the planet until it met on the opposite side with what would later be described as a "reverse rainboom."

The last thing Twilight saw before falling unconscious was the Doctor's wonderful smiling face.


	5. Onwards!

**Chapter 5: Onwards!**

Twilight came to slowly, the weight of the Tiara of Magic on her head confusing her before her memory of what had happened moments ago had returned.

The Doctor had already awoken, and was now happily running from one unconscious pony to the next, taking readings from his sonic screwdriver.

"Brilliant!" he beamed, seeing that the six mares were stirring. "I almost don't believe it! All the Ponyville ponies are safe, completely unharmed with no signs of alien influence!"

"You mean…it worked?" Twilight asked.

"Wonderfully!" he replied, gleefully jumping around the room, giggling to himself.

"I _think_ he got a little too much of Pinkie's Element," said Rainbow Dash.

"No, silly-filly!" said Pinkie Pie, joining the Doctor as he bounced, "It's juuuust right!"

The other five mares couldn't help but laugh at the two ponies' antics. The Doctor calmed down soon afterward, but Pinkie continued on, not caring that she was alone in her frivolity.

"Congratulations, Doctor." Celestia's kindly voice turned their attention to the doorway she and her sister were walking through, prompting the seven ponies to quickly bow. "I must admit, we were worried whether your plan would succeed or not."

Luna scoffed at this. "_You_ were worried, sister; _I_ was telling you everything would be fine."

"Either way," Celestia laughed, "you've defended Equestria from a great danger, and for that, we are in your debt."

"It was my pleasure, your highnesses." said the Doctor, dipping his head.

"Ooh! Ooh! Ooh!" Pinkie Pie appeared between them, bouncing excitedly. "I know how we can thank him! _A PARTY!_"

* * *

><p>By the time the evening arrived, all of Ponyville had prepared for the celebration. Many ponies had tried to bring gifts, but when the Doctor politely refused them, they returned with the next best thing: food.<p>

The Doctor had eaten at parties on hundreds of planets, but the Ponyville cuisine surprised him. Everything tasted spectacularly delicious – especially the bananas, which he requested to have several crates full of to take aboard the TARDIS.

Throughout the night, ponies crowded around him, asking him questions about himself and how he saved them. The six Element-bearers also had their own share of topics they wished to be cleared up.

"So Doc," Applejack said, "When you came on into town, why did ya show me a blank card?"

The Doctor nodded in acknowledgement as he finished his cupcake and gave a compliment to Mr. and Mrs. Cake, who had made it their job to make sure that his plate was never empty. "Actually, Applejack, it wasn't blank – well, it wasn't supposed to be." He dug into his new saddlebags (the only gift he had accepted, as they were designed by Rarity and she wouldn't take no for an answer) and pulled out the card. "This is my psychic paper. Says anything I want it to. It's a very nifty little thing; I've been thrown in jail a lot less since I started carrying it around."

"So, then how was she able to see through it?" Rainbow Dash asked. "I mean, it fooled Twilight, and she's the nerdiest of us all."

"Well, she's the Element of Honesty, isn't she? Looks like that also makes her a living lie detector."

The night carried on, and soon thoughts of bed could no longer be ignored and slowly the party began to dissipate.

The Doctor had slipped out amidst the clean-up and stood on the hill where he had parked the TARDIS. The sun had not risen just yet; the stars and moon were shining their last before the new day.

His eyes were closed as the blue box hummed softly next to him. He knew _that_ part of travelling and meeting new people was coming up, the part that never failed to make him anxious because the result was never certain: the inevitable question.

"You're leaving?"

The Doctor turned to see the six mares, along with the two princesses, had gathered behind him, all with the same sad look.

He gave them a soft smile. "Yep; I don't make a habit of staying in one place too long. The universe isn't going to explore itself, you know."

"But you've barely been here a day," Twilight pleaded. "You're welcome to stay as long as you want."

"Twilight…" the Doctor said slowly, "There are millions of people out there, all waiting for a knight in shining armor to step in and save them, and all they're ever going to get is a daft old man in a stolen box, or nothing. No matter how much I want to stay, I can't abandon them."

The groups' eyes lowered in disappointment. "So…this is goodbye?" Fluttershy asked, tearing up.

"Looks like it." The Doctor's expression suddenly turned sly. "Unless, of course, you want to come with me."

The mares' heads shot up. "You mean it?" Rainbow said excitedly.

"You've been inside. I could fit all of Ponyville if I wanted to."

The mares gave cries of joy and shared high-hooves, but Twilight's expression suddenly faltered. "But I have to manage the library…and Applejack has to help Big Macintosh at Sweet Apple Acres, and Rarity has her boutique, and…we all have responsibilities here." She sighed. "I'm sorry, Doctor, but…I'm afraid we can't."

The Doctor merely shrugged at this. "Alright, I understand. You can't just drop everything to go adventuring." He opened the door to the TARDIS and stepped halfway in. "Of course, she does also travel through time, but it's not like that changes anything…"

Twilight blinked. "Wait, what was that?"

The Doctor shrugged again, his confident smirk growing. "Oh, I was just saying that the TARDIS is a time machine, so we could take a trip around the solar system and be back in time for tea, but you've already said you can't go, so I'll just –"

The six mares crowded the doorway with huge smiles on their faces. The Doctor laughed. "I'll take that as a yes!"

Twilight bounced around, giddy as a schoolfilly. "Yes! Yes! Yes!" She stopped a split second before colliding with Celestia. "Um – I mean, if it's okay with you, Princess Celestia."

The Princess smiled warmly. "It's not my decision, my faithful student. I'm sure that this will make for some very interesting reports on the magic of friendship." She turned to the Doctor. "You will make sure her letters get to me, won't you?"

"I'm sure I can work something out," the Doctor replied. "Trans-spatial communication is one of my specialties, after all. That and running, there's an awful lot of running."

Celestia nodded. "Then allow us to give you a parting gift."

Celestia looked to Luna, and their horns began to glow in unison. The horizon changed as the sun and moon answered their call and brought dawn to the citizens of Equestria.

In the back of the Doctor's mind a million objections fired off, arguing that what he was seeing was impossible, that it went against the basest rules of the universe, that it was just so _wrong_.

But when he spoke, only one word escaped his lips: "Beautiful."

* * *

><p>Spike was awoken from his post-party nap by Twilight bursting through into the library. He groaned as she merrily ran around the hollow tree, taking all kinds of objects placing them in a suitcase.<p>

"Spike I'm going to be gone for a while," she said as she browsed the shelves. "You'll need to watch the library for me; get along with Owlowiscious and don't eat all the diamonds, alright?"

"Uh, sure," the dragon replied. "But, where are you going?"

"I don't know."

"Okay…when will you be back?"

"I don't know."

Spike narrowed his eyes. "Wait. You're going on a trip, but, you don't know where you're going or when you'll be back?"

"That's the beauty of it, Spike!" Twilight said happily. "An expedition into the unknown, guided by the Doctor, the only pony who's seen it all! It'll be fantastic!"

"Listen to yourself, Twilight," said Spike. "You're not making any sense. You just met the Doctor yesterday. You barely know who he is!"

She stopped at the door and gave the dragon a confident grin. "Then I'm about to find out."

Twilight stepped out of the library and ran to join her friends, old and new, on an adventure unlike any other.


End file.

Doctor Who, My Little Pony, Fantasy, Sci-Fi