Thought Given Form

by Coffee dot exe

Rating: teen
Tags: Crossover, Doctor Whooves, Lyra, My Little Pony: Friendship is Magic, Dark, Comedy, Other, Adventure
Length: 2129

Citizens of Ponyville are slowly disappearing. It's up to one pony and his blue box to discover the secret.

The Doctor has just regenerated into his eleventh incarnation, and upon his arrival he meets a new pony to call a friend. A heartbroken mare. But before he is able make a proper introduction, they learn of a new threat to the small town of Ponyville. Citizens are disappearing left and right with no evidence as to where they've gone or who ( or what took them). It's up to the mad doctor and his new friend to unravel the mystery.

Published 2013-07-26 06:30:02 UTC
Last updated 2013-07-26 06:30:02 UTC

A New Doctor, A New Threat

“I don’t want to go...”

The Doctor muttered the words to himself as he fell to the ground in a sweat, feeling the Time Lord energy flow through him rapidly. He flinched as a sharp pain flew through his brown, stallion body. He knew what was coming, but he didn’t have to enjoy it.

The energy became too much for the doctor to handle as he stood rigid in his TARDIS. The golden energy burst from his body, engulfing every inch of him. With the visual beauty of what could only be described as a space-time hydrant bursting, the energy flowed out of him and struck the walls of his time machine. He shouted in pain as his body began to morph around him.

The TARDIS began exploding around The Doctor as he came down from his regeneration high. He fell to his knees, breathing heavily. He began looking around, smiling. He reached up with his hooves to feel his face and body.

“Ok then, let’s to a head count!” He touched his head and swatted the area around it. “One! Good! Just the way I like it! Lonely,” he said cheerfully.

He looked down at his hooves, “Still a pony, I guess that makes sense. I miss the thumbs though. Oh, I changed color! I’m tan? But I want to be orange! I hope my next time I’m orange!”

He felt his mane. “Am I a mare?” He quicky looked down his body. “Nope, flat as a board.”

An explosion behind him startled him as he hopped to his hooves. He dashed over to the screen in the center of his time machine. He flung his head forward to read what the screen was flashing only to be met with a loud “pang” and a searing pain in his head. He stumbled after the blow to the head and tried to regain his footing. The TARDIS lurched downward and the Doctor braced for impact with the floor. He did not feel the impact though.

“Why am I not on the ground?” he asked himself, as his head darted around. A flapping noise is heard and he turns his head around.

A pair of tan wings flapped from his back to his wonder. “Wings? I’m a pegasus now? How exciting! I wish I was a unicorn though, so I could properly hold my soni-”

He suddenly lost control of his wings and fell to the ground with a peculiar crunch.

“Oh no, I crushed the screwdriver..” He said, exasperated.

The TARDIS rocked violently as he stumbled towards the console.

“Priorities! Seems like I’ve lost my sense of them. Got to land the girl before she blows a fuse! Dimitte Praeterita!” He shouted excitedly.

He steered the blue box towards an open field. Loud pops and hisses were coming from the walls. The TARDIS whizzed past many ponies homes, fire spewing from the broken windows.

~

It was just about time for the young mare to hop into bed to rest up. She smiled as she snuggled under her warm blankets. Just as she got her eyes closed, a loud mechanical whirring noise followed by a loud crash woke the unicorn. She jumped to her window to see a large blue box crashed sideways in her front yard.

“What in Equestria..?” She asked herself, making her way downstairs and outside. As the unicorn opened her door, the blue box swung open, water pouring out of the opening. She gasped as a tan unicorn popped his head out, soaked head to toe.

The Doctor looked up at the teal pony and smiled goofily. “Oh, hello!”

“Hi?” The mare replied, not knowing what to think of the situation. “Who are you and why is this giant box thing in front of my house?”

“To answer those, in order, Because it crashed, and I’m The Doctor!” He said happily. “Wait, flip those. And who might I have the pleasure of speaking to?” He smiled innocently.

“My name is Lyra.”

“Lyra?”

“You got a problem with my name?” She protested.

“What? No, course not! Lyra’s a perfect name! Especially for a mare!”

She looked the pony up and down. “Uh huh, why are you soaked?”

“I got covered in water.”

“How?”

“Water splashed onto my body. Is this a hard concept to grasp or something?”

Lyra facehoofed and sighed. “Look can you get this...” She paused to collect her thoughts.

“TARDIS?” He interjected.

“Whatever it is,” she sighed, “Just get it out of here.”

The Doctor frowned at her. “You look like somepony broke up with you.”

Lyra’s face went deep red. “No I don’t!”

The Doctor tilted his head at her. “Course you do. I’ve seen heartbreak happen. I’ve felt it myself,” he said. “And your face and body are telling me your fillyfriend left you.”

Lyra grabbed the tan pegasus by his tie. “Who told you?!” She yelped.

“Two ponies,” he said simply. “Well, one if you want to get technical.”

The unicorn’s jaw dropped. She gawked at him in disbelief. “What are talking about??”

The Doctor smiled at her. He pointed his hoof at Lyra’s face. “Well first your face said it. Then, you said it just now.”

“... I’m talking to a mad pony that fell out of a blue box.”

“Wanna ride?” He asked slyly, winking.

She gasped and smacked him across the face. “It Was Two Days Ago!!”

The Doctor squinched his nose and shook his head due to the slap. “I know that. I was talking about riding in the box. Nopony can frown while riding in a TARDIS for the first time!”

She squinted her eyes. She gazed over to the sparking box. “I’m not riding in that death trap.”

The pegasus pouted. “Sexy is not a death box,” he protested, “ I promise you’ll enjoy it!”

Lyra gave the The Doctor a deadpan look before she let go of his tie.

He dropped to the ground with a soft thud. He popped back up onto his hooves and trotted over to the TARDIS. “Would you be willing to use your magic to help lift her up for me?” He asked Lyra, motioning to the sideways phone booth.

Lyra sighed. “Whatever,” she said, exasperated. She pointed her horn to the blue box and an aura surrounded it. She nonchalantly began to lift it. A stressed expression shot across her face as soon as it left the ground. “The buck is this thing made of?” She asked, struggling to hold it up.

The Doctor began to wiggle his wings to gain control of them. The wings jerked and moved as he tried to get the motion of flapping down. “These will take some getting used to.” He said, curiously flapping them.

The TARDIS finally lands on its base and Lyra lets out a sigh of relief. She plops to the ground, exhausted. “Seriously, what do you have in that box?”

“Do you want the long list, or the short one?” The Doctor asked, dusting some dirt of the blue box with his wings.

“Neither? Both? Whatever.” Lyra shrugged.

“Long it is!” The Doctor exclaimed, as the teal unicorn let out a groan.

“I have control panels, evening flannels, swimming pools, kitchen stools, coffee tables, sleeping stables, electric cables, trees of maple, telephones, dinosaur bones, wardrobe closet, whosey whatsits, big library, Richard Scary, and an infinite amount of storage space. Pretty much anything and everything you’d ever need when traveling through space and time!”

Lyra sat gawking at the Pegasus in front of her, all while The Doctor stood before her smiling gleefully.

“Did you say time travel?” Lyra asked in disbelief.

The Doctor smiled as he tapped the side of the box with his hoof, “I did! I’m a Time Lord!”

Lyra opened her mouth to respond, but was interrupted by a shout. She and the Doctor turned to see a white unicorn approach them in royal guard armor.

“What are you doing out?” The guard barked at the two ponies.

“AH! A guard!” The Doctor cried cheerfully. “Equestria’s finest, if I do say so myself. I quite enjoy the mohawks!” He reached forward to play with the guards military style mane.

The guard avoided the tan earth pony’s hoof and pointed its horn at the pair. “It’s past curfew! You two should be inside now.” The guard said sternly.

“Curfew?” Lyra asked. “Why would there be a curfew?”

The guard huffed at them. “Have you two not been paying attention to any news? Recently, something has been going on around town, ponies have been disappearing mysteriously, and it’s gotten to the point where us guards had to come down and enforce a curfew to avoid any more disappearances.”

The Doctor and Lyra shot each other concerned looks. “Disappearances?” The Doctor asked.

The guard nodded. “Five ponies have disappeared without a trace. Nopony has a clue where they could have gone.”

The Doctor brought a hoof to his mouth, tapping his nose in thought. He then grinned wide and extended the hoof to the guard. “Well, you should feel lucky. I’m the Doctor!”

“Doctor Who?”

“Just ‘The Doctor’!” He said cheerfully. “I fix things.”

The guard looked down at him, confused. “What kinds of things?”

“All kinds of things!” The Doctor replied, surveying the area around them. “Big things, Small things, Things that climb on rocks.”

The guard gazed at them hesitantly. The Doctor raised a brow.

The guard stared long and hard at the Doctor, questioning his cheerful demeanor. “You’re free to look around all you like, but if any of the other guards catch you out at night, you’re on your own.” The guard huffed as he jabbed his hoof into the doctor chest and heading off.

“There we are, that’s why I love it here in Equestria!” Piped The Doctor, “Always something interesting going on!”

Lyra gave The Doctor a confused look before shaking her head, “Alright then, you’ve got your box and something to do, now could you get the box off my lawn?”

The Doctor turned, “What? You don’t wanna join?”

“No way. Ponies are disappearing left and right, I’m not gonna risk my tail at night if there’s a ponynapper.”

The Doctor tilted his head and trotted over to Lyra, “Ah come on! Where’s your sense of adventure? You gotta have something to do to keep your mind off your recent lifestyle change!”

Lyra tensed up, about ready to kick the insane pegasus. She stopped though. She closed her eyes and took a long breath and turned to him, “If I do, will you please take your box off my lawn and leave me alone?”

The Doctor nodded and used his wings to cross both sides of his chest. “Cross my hearts and hope to die.. er... regenerate!” He smiled and began to head out to investigate.

Lyra raised an eyebrow before shrugging and catching up to the mad pony.

~

Meanwhile, across town, shouts were heard from inside a cottage. The door flew open to reveal an earth stallion shouting up the stairs, clearly in a drunken stupor.

“I don’t need this from a mare like you!” he shouted as he stumbled out the door. “I work 40 hours a week at that farm and I get lip from you the second I’m home? No way!” He slammed the door behind him and began fumbling down the street.

Not long after, the stallion noticed he didn’t recognized where in town he was. No street lights were on, everypony was asleep in bed, and there were no guards in the area to direct him on where to go. He spun around quickly, trying to decipher his location.

Then he heard leaves crunching. He turned towards the noise only to see an empty street. He shrugged and continued his walk. A few minutes later the crunching began again. He turned even quicker and saw a shape. He squinted at it and made out the basic shape of a tall stallion staring at him.

“The buck are you lookin’ at, short stop?” He taunted, trying to drive the tall pony off. He turned around only to hear more crunching.

He became enraged and spun around quickly and shouted, “You Got A Problem???” There was nopony to be found. He shrugged and turned to see the silhouette of the stallion coming at him rapidly It was clearly moving fast, but its legs remained stiff.

A stifled scream was heard from outside the houses of the ponyville residents. When the neighbors stepped out to see what had happened, there was nopony to be found. The only clue anypony had found was a symbol burnt into the ground. A symbol resembling a circle with a large X through it.