Doctor Whoof: The Iron Horse

Chapters

Prologue
(Part 1) Calm before the Storm
(Part 2) Old and New
(Part 3) To hunt a Cyberpony
(Part 4) Facts, Figures, and Failures.
(Part 5) The Medicine Pony and The Grey Queen
Torchwhoof Files: Derpy Hooves and C.M.C.-1 (Apple Bloom)
(Part 6) The Grey and Unseen Armies
(Part 7) Hoof Full of Bits (or, The Good, The Bad, and The Mechanical)
Epilogue

Prologue

Two weeks after Time of the Hourglass...

“Ow! Blasts!” The Doctor grabbed his hoof and stuck it in his mouth, sucking on it to stop the pain. He had just burnt himself on the Time Cortex Heating Agent, something he had never done before when he had hands.

“You ok?” Derpy asked, her wing folded over a small tool box her time colt friend put her in charge of. The grey, wall-eyed pegasus hadn’t stopped helping The Doctor for the past three days. Thankfully, Dinky loved exploring, as she called it, ‘Mr. Doctor’s silly blue box’, and that kept the filly entertained for a while. Derpy was happy that her daughter was quick to befriend the time traveling pony, even taking him on as sort of a father figure, but even then the mail pegasus knew her little muffin’s happiness wouldn’t last forever. The Doctor wanted to go home, and nothing would stop him.

“Yeah, I’m fine. Just got burnt a bit, nothing new.” The Doctor lied. He thought he was getting used to this strange pony body, but little mistakes like that told him otherwise. It was like it was rejecting him, trying to push the time lord out of his and turn him into a normal Equestrian. He couldn’t even eat his Jammy Dodgers any more because of his awful pony teeth, and he couldn’t even bring himself to mention the apples. He was starting to hate them more then pairs... Ok that was a bit of a lie. The time colt shook his head a bit and looked down at his companion, “Derpy, could you hand me the Screwdriver?”

The grey pegasus reached into the tool box with her mouth and pulled out the long, metal object. She slid it under the TARDIS consol, but a few moments later it was tossed back at her hooves. “The other one?”

“The other one.” The Doctor replied, now feeling his Sonic Screwdriver being tossed at his right front hoof. He placed the device in his mouth and slid it over the giant hot plate. It was strange how just two weeks ago, he and a group of ponies took down one of the last Time Lords. What surprised him even more was how intact her TARDIS was, even after being turned into a pony robot. He managed to salvage a few parts from it, but nothing powerful enough to fix the troubles with his Time Cortex. As for The Rani, The Doctor hopped that it wasn’t just alicorns who could breath on the moon.

Suddenly, the sound of tiny knocks came from the TARDIS doors. Before the brown time colt could move though, the doors where flung open to by the Cutie Mark Crusaders. Just seeing the three fillies made The Doctor worry, but what they shouted out next made him absolutely terrified.

“Cutie Mark Crusaders! TARDIS Repair Mares!” Apple Bloom, Scootaloo, and Sweetie Belle called out in unison. The three then stampeded to the consul and started pressing random buttons, making remarks like ‘Maybe this’ll work!” which was always followed by a small set of sparks and Scootaloo saying ‘Nope.”. Finally, after twenty failure, The Doctor had had enough.

“Girls!” the time colt yelled, causing the entire TARDIS to become silent, “Listen... Maybe you should go and find Dinky.”

“Awww, but that sounds boring.” Scootaloo remarked, her eyes drifting towards the shinny buttons once again.

“Wait!” The Doctor stood, hitting his head on the metal consol and groaning in pain, “How about...uh... Cutie Mark Crusaders Search Party?”

“Yeah!” Apple Bloom said, looking at the other crusaders, “Let’s go girls! There’s a filly who needs our help!”

“Cutie Mark Crusaders! Search Ponies!” The three yelled out, then raced towards one of the open hall ways. The Doctor wiped the sweat from his forehead and sighed, as much as he liked the three fillies... They where more then a hand full. Or hoof full, as it where... He still couldn’t get used to the Equestrian sayings.

***

A breeze rushed through the back alley of Appleloosa, kicking up a small cloud of dust that spiraled back to the ground quickly. Suddenly, the hoof beats of a yellow earth pony in a vest and brown Stetson broke the silence of the small road. In front of him was a pony in a cape and hood, a pony who had been sighted at two foalnappings in the same area. As the new deputy of Appleloosa, Braeburn felt it was his duty to catch this suspect. Behind his was his partner, and lover, Little Strongheart, who had spotted the cloaked pony first.

“You cut around the other way Lil!” the Apple pony called out, “Cut him off at the past!”

“Got it!” the buffalo called out, her hoof beats getting softer as she sped to the next street. She knew that her beloved’s plan would work out, no one knew Appleloosa like Braeburn Apple. However, once she got to the other end of the alley the cloaked figure had stopped and just stood there. It looked to her, then back and the deputy pony, a small humming noise coming from under its hood.

Braeburn took a step forward, “We just want ta ask you a few questions partner.” he began, “First off, who are you?”

The hooded pony stayed silent, until it’s eyes locked onto Little Strongheart. Then, in a cold, unfeeling voice it said only one word. A word that would haunt Appleloosa, and Braeburn, for the rest of time.

“Delete.”

(Part 1) Calm before the Storm

Calm before the Storm

“And... Done!” The Doctor called from under his consul, “Ok Derpy, flip the red wobbly thingy on me signal and not a moment too soon. Ready? Three... Two... One... NOW!” The time colt flew from the middle of the room, just as his assistant pulled the strange red slider down. But nothing happened. “What? That’s it?!” The Doctor yelled as he walked towards his machine, “Not a blip? Not even an explosion?! Really?! Is this bloody place messing with you so much that you can’t even blow up?” The brown pony then kicked the metal, which sent a quick shock of pain up his leg. “BLOODY HELL! You damned piece of...”

“Doctor stop!” Derpy Hooves quickly wrapped her front hooves around her friend, trying to calm him down before one of the foals ran in and saw his tantrum. Slowly, The Doctor’s two beating hearts calmed and he pulled away from the grey pegasus.

“Thank you Derpy... I needed that.” he said, then quickly returned to his work. The time colt began to push what seemed like random buttons to Derpy, but she was sure her friend had a pattern of some sort. Finally, the brown colt just shook his head and sighed. “She’s fried Derpy, completely gone. I thought that the pieces from The Rani’s TARDIS would help stabilize her but... Wait, that’s it! The Rani!” The Doctor turned to Derpy and smiled wide, then ran for his bow-tie, “If I could just get her to tell me how her TARDIS stayed relatively unscaved, then I mite have a chance of getting home by tonight!”

The mail pegasus could only smile, as if this was the best news she would ever get. However, in Derpy’s heart she was truly afraid of The Doctor leaving. But how could she tell him? How could she tell her best friend that she couldn’t let him go, that she never wanted to let him go. Not after all they’ve been through.
“It’s not up to me though...” Derpy said to herself.

“What was that?” The Doctor asked.

“Nothing... Just be careful ok? The Rani’s probably still pretty mad at all of us.”

“Oh don’t worry,” The time colt smiled as his friend confidently, “I’ve dealt with her before.” Then, The Doctor headed out the door and left Derpy behind. Once the pegasus knew her friend was gone, Derpy kneeled under the TARDIS consul. She then carefully gripped a wire with her teeth, and reconnected it to the red wobbly thingy.

“I shouldn’t have done that...” Derpy said to herself, her eyes tearing up as she heard the Cutie Mark Crusaders and Dinky run outside.

***

The Doctor felt his shoulders crack as he moved them, then he entered Ponyville Town Hall. The tall, tower-like building had a new coat of bright yellow paint on the inside, with Mayor Mare’s office just beyond a flight of white stairs. The Doctor began his accent on the staircase, noting the various pictures and awards on the walls. He was actually able to spot himself in quite a few, and Derpy too if he looked hard enough. One picture caught his eye though, the picture of him and River Song in her pony form. It was torn from a newspaper article that read Heroes save Ponyville: Who is the mysterious Doctor Whoof?This made the old time colt chuckle a bit. It was strange how humans had barely gotten a picture of him, and yet these ponies had at least ten or fifteen. The Doctor pushed it to the back of his mind and made his way to the mayor’s office.

“Hello again Mayor, I’d like to see our favorite prisoner.” the brown colt said as he pushed through the large white doors of Mayor Mare’s office. However, he wasn’t greeted by just the mayor, but also a white unicorn in black armor. To Just by his appearance, The Doctor could tell that the unicorn was battle hardened, mostly due to the three long scars on the armored pony’s right eye.

“Oh, Doctor...” Mayor Mare said, her voice sounding a bit shaken, “This fine gentlecolt was just asking me about you.”

The unicorn stepped forward and nodded to The Doctor, “The elusive Doctor... We meet at last.”

“Yes... And you would be?” The time colt asked.

“Oh yes, where are my manners? I am General Stormbreaker of the Canterlot Royal Guard.” The armored unicorn answered, “I’ve actually been promoted to a new station quite recently, and it’s really all thanks to you and your friend Miss Rani.”

“Really? Friend?” The Doctor cocked his head to the side.

“Oh come now Doctor, you don’t have to play coy with me.” Stormbreaker smiled, which did nothing to ease his menacing looks, “The Rani told us of your past friendship, but I’m willing to over look obvious lies if you’re willing to answer some questions.”

“Now wait a moment General,” Mayor Mare piped up, having found her courage once more, “you may be part of the royal guard, but I will not stand for you blackmailing a citizen of MY town. Do you understand?”

For a moment, it looked as if Stormbreaker was going to hit the mayor, but somehow the battle worn colt held his temper at bay. “I can assure you, Miss Mare, that I can question whomever I please.” The general turned back to The Doctor, “And I’m sure neither of you will mind if I take The Rani into Canterlot dungeon now. After all...” Stormbreaker paused and looked The Doctor straight in the eye, “We don’t want another incident, do we Doctor?”

The time colt glared at this new face, noting how the right eye seemed to be blind and scared. “No, we don’t...” he replied, then Stormbreaker began to leave. “Before you go, I want to know something. Which branch of the royal guard are you in exactly?” Stormbreaker turned and smiled once more, this time a malicious and hate-filled smile.

“I’m the head of Torchwhoof.” the general replied, then left. As soon as he was out of ear shot, Mayor Mare stepped to The Doctor’s side.

“Doctor, What is Torchwhoof?” she asked flatly.

“Trouble.” The Doctor answered, his eyes burning with hate as he realize what his presence had done to Equestria. “And it’s all my fault.”

***

Apple Bloom loved the feeling of the wind running through her hair as she ran, especially when it was accompanied by the smell of her family’s home grown apples. The filly couldn’t help but laugh as she chased after Scootaloo and Sweetie Belle, their game of tag had been going on for what felt like seconds when it was actually an hour. They had asked Dinky to join them, but the shy unicorn opted to help Granny Smith cook up a big dinner for everypony. The Cutie Mark Crusaders didn’t pursue the matter, they knew that Dinky was just trying to get the same thing they where. A Cutie Mark.

Derpy was helping Applejack finish bucking her side of the orchard, while Big Macintosh was relaxing after finishing his own chores. The three eager fillies had asked to help, but all three adult ponies vigorously said no. The CMCs where used to that, especially after last week when they had almost broken Big Mac’s leg, but it didn’t bother them. It just gave them more time to play, at least until Sweetie saw a mail pegasus fly up to the farm house’s porch. Each filly looked into the other’s eyes and smiled, all mouthing the same thing.

“Cutie Mark Crusaders! Ninja Ponies!” The Crusaders called out silently. They kept their bellies to the ground as they snuck up on Big Mac and the mail pony, able to hear their conversation easily.

“So,” the mail pegasus began, his voice had a slight Stalionguard accent, “you’re cousin needs a bit of help, dah?”

“Eeyup.” Big Mac replied, seemingly relaxed around this mail pony. “Braeburn’s always needed a bit of help sometimes Dimitrot.”

“I completely understand, my brother’s the same way.” Dimitrot said, “But from what you told me yesterday, you and Miss AJ wont be able to finish the apple bucking in time.”

“Eenope...” Macintosh nodded, then looked at the tall grass behind his friend, “Apple Bloom, ya’ll want ta go see cousin Braeburn and Little Strongheart in Appleloosa?”

At that point, Apple Bloom blew the Cutie Mark Crusader’s cover completely. She jumped up and ran towards the porch, “Heck yeah I do! Um... I mean... Eeyup.” The filly mimicked her big brother almost perfectly, causing Dimitrot to laugh. The mail pegasus said his good bye and flew off to deliver more mail, leaving the three fillies with the big red colt.

“Now, you’re gonna need somepony to go with you... Not you two girls, a full grown pony.” Big Mac said, squashing Sweetie Belle and Scootaloo’s hopes of going with. Suddenly, The Doctor walked past the small group, a sour look on his face as he entered the Apple’s house. “Well, he don’t seem like he’s too happy now. Wonder what that Ran-knee said to him?”

“Big Mac,” Apple Bloom said, smiling wide, “I know just the pony to come with me!”

Author's Note: It's Doctor Who trivia time again! Just some stuff to explain things that... Well, that I feel like explaining. To those who watch Doctor Who, the name Torchwood sounds a little familure (unless you've only started watching durning Matt Smith's run). Torchwood (an anagram for Doctor Who), is an agency started by Queen Victoria after her run in with The Doctor when he was in his 9th incarnation (before David Tennet). It's main purpose is to study alien technology that comes to Earth to help get mankind ready incase a large scale alien invasion occurs.

Torchwood's had two main 'leaders': Capt. Jack Harkness (an old ally of the Doctor's who's in charge of Torchwood location 3), and Yvonne Hartman (who is the first person seen in the Doctor who series as the head of Torchwood.) Torchwood operates above even military level, which is the same for Torchwhoof.

As for General Stormbreaker, he's not based off either Harkness of Hartman. I actually used a pony from the Tumblr for Little Miss Rarity, so yeah... Just wanted to clear that up. As for what Torchwhoof was made for... It'll be explained later on.

Thanks for your time and support,

Muleicous.

(Part 2) Old and New

Old and New

The Doctor yawed as he stared out the window of the train. Normally, he would be questioning how a team of no more then four horses was able to pull a train, let alone a train full of ponies. Today, however, his mind was focused more on Torchwhoof, and General Stormbreaker.

I understand why Celestia and Luna would make a division of the royal guard to over look strange events, the time colt thought, but even in my own dimension that took millennium to come about. This universe is strange, even for me, but first the pictures of me in city hall, the news paper clippings, and now Torchwhoof? It’s like there’s some force pushing all these events in order... Could it just be my presence here?

“Hey Doctor?” Apple Bloom’s voice shattered The Doctor’s train of thought. This whole time the filly had barely made a peep, so the brown stallion wrote her off as being asleep.

“Yes Apple Bloom? What’s wrong?” The time colt turned his head to face the farm filly on the bench across from his own.

“Nothing, I was just wondering why you didn’t ask Derpy to come with us.” Apple Bloom smiled at her friend, she really hadn’t talked to The Doctor alone since she met him. Maybe she’d be able to learn more about the mysterious pony with the blue box.

“I did actually,” The Doctor began, “ Derpy thought the trip would be too long to stay away from Dinky. Plus, she didn’t want to pull her daughter out of school, so she just wished me a safe trip.” He smiled as he pictured the glee-filled, yet still sad look of his companion. He knew that the grey pegasus would miss him, and he’d miss her too, but Apple Bloom did need someone... no, somepony. Blasted Equestrian phrases... to watched her and make sure she didn’t get hurt. Or as Big Mac had put it, ‘Don’t let her try any Cutie Mark Crusades.’ The Doctor couldn’t help but chuckle at the big red stallion’s plea, he knew that Apple Bloom wouldn’t try anything with out her two best friends. It actually made the time colt wonder how destructive the three fillies would be apart... He shivered as he imagined a completely destroyed Sweet Apple Acres, Carousel Boutique, and...

“Hey Apple Bloom, where does Scootaloo live?” The Doctor asked, his curiosity peaked as he knew very little about the stunt loving pegasus... other then her hero worship of Rainbow Dash.

“With her mom in Cloudsdale.” the farm filly giggled a bit, “Where did you think silly?”

“Well, I’ve never asked her anything... And you and Sweetie Bell live in town. I half expected her to be living with Rainbow Dash.” The time colt chuckled, but stopped as his young ally spoke up.

“She and Dash do live together some days... She and Scoot’s mom are together.”

“Ah... That explains why she worships Rainbow Dash so much... Father figure...” The Doctor mumbled.

“What?” Apple Bloom asked, suddenly her eyes caught sight of a familiar groove of trees. “Hey! There’s the fields, we’re almost there!” The fillies eyes stayed glued at the scenery just outside as she combed the field, looking for any sign of her sister’s old tree, Bloomberg. The Doctor wiped his forehead, sighing as he dodged that big bullet. As he looked out the window, the time colt noticed how the plains filled up so suddenly. Before, they had been rolling through a nearly endless desert, but now it was like the two ponies had pulled into an oasis.

“An apple filled town in the middle of a gigantic bad-land,” The Doctor said to himself, “this place really is amazing.”

***

“Welcome to AAAAAAAAAAAAPPLELOSA!” a voice called out from the platform. As the two ponies stepped off the train, followed by the other hundred or so Equestrians around them, Apple Bloom spotted the familiar Stetson of her oldest cousin.

“Braeburn!” the farm filly called out, quickly running to a ginger pony with a pale yellow coat similar to the young filly’s. The colt, surprisingly not a Clydesdale as The Doctor expected, also wore a vest with a small silver star pinned on it.

“Well howdy cousin Apple Bloom.” Braeburn picked up Apple Bloom with his front hooves and tossed her in the air, catching her quickly and setting her down before his eyes met The Doctor’s. “Oh, howdy there. I’m guessin’ you’re the pony that from Big Mac’s letter? The Doctor right? I’m Braeburn Apple.” The cowpony offered his front hoof, which the Doctor took in the strange Equestrian shake he had never grown accustomed to.

“Um, yes, it’s good to meet you.” the time colt’s mind was focused on how Braeburn could’ve pinned his star on if he didn’t have magic, “Apple Bloom tells me that you’re the deputy here. All thought it seems pretty quiet.” Just as The Doctor finished his sentence, he noticed a deep frown on his new friend’s face.

“Well, that ain’t because of how good of a job the sheriff and I are doin’.” Braeburn turned to the dusty little town, “That’s actually the reason I sent the letter to cousin AJ in the first place. I was hopin’ that she and her friends or Big Mac could come and help me with this case I’m workin’ on, but, from what Big Macintosh wrote, I think you could help me a lot, Mr. Doctor.”

“Please, just call me The Doctor.” the time colt said, “No need for formalities, any family of Apple Bloom’s is a friend of mine.”

“Same to ya’ll,” the deputy pony smiled and walked down the stairs of the small, wooden train station, “I’ll tell ya’ll about our little... problem at the sheriff’s station.”

***

“So,” Braeburn said as he and the two Ponyville ponies walked into the small sheriff’s office/jail, “over the past month or so, we’ve been gettin’ reports of foalnapping’s from all over the area. Even the buffalo have had their young stolen from them in the night, so they’ve given us as much help as possible. I’ve even been working close with one...”

“Little Strongheart?” Apple Bloom interrupted, nudging The Doctor, “His girlfriend.”

“Apple Bloom hush!” Braeburn said, his face turning as red as Big Macintosh’s, “But... yeah, she is. Me and her where chasing down a suspicious pony the other day, some colt in a big black cloak. A few other ponies said they had seen the same pony in the area on the nights of the foalnappings, so we just wanted to talk to him. We chased it down a back alley... We even had it cornered....”

“It?” The Doctor asked, “So it wasn’t a cloaked pony?

“I... I don’t know what it is...” Braeburn sat on the floor, shaking his head as if her where in shock, “It had these... Black eyes. Completely black, and it looked like a... A suit of old Equestrian armor. You know, like the ol’ Knights of the Celestial Order stories.” The cowpony began to shiver like a squirrel in a snow bank.

“Braeburn?” Apple Bloom put a hoof on her cousin’s back, “You don’t have ta finish...”

“No! No...” Braeburn patted the little filly’s head, “I... I need ta.” He looked back up at The Doctor, “It looked at Lil, and just ran after her like a pony possessed. I chased it, bucked it in the plot,” the deputy smiled softly and lowered his head, “nearly broke my legs on it’s hide. The thing tumbled head over hooves and went through a wall of one of the houses... Then just stood up and walked towards me. It... It said something... I didn’t hear what, but it fell down after that. Hasn’t moved since... Lil and I put it over there...” Braeburn pointed one of his front hooves as a covered up figure in the cage near the back of the sheriff’s office.

The Doctor slowly edged his way to the iron bars, stopping only to have Braeburn unlock the cell. “Becareful Doc...” the cowpony said, as the time colt stepped into the cell. The Doctor leaned down and gripped the silky cloak in his teeth, then pulled it back fast. Under the cloak was a pony, at least what used to be a pony. It was metal, all grey in color with a blank, emotionless expression on it’s face.

On it’s head where two small, pointed horns. Right bellow them where it’s eyes, which where just as Braeburn said, blank and empty. The Doctor knew what this creature was, he had hopped that it would never get close to Equestria. However, it was here, staring him in the face as he was only 100 miles away from Ponyville. “No...” The Doctor shook his head and took a few steps back, his face a painting of fear.

“Doctor?” Apple Bloom asked as she stood behind her cousin, seeing the face of the metal monster staring back at her, “What is that?” The Doctor turned to his companion and the deputy and uttered only on word:

“Cyberman.”

(Part 3) To hunt a Cyberpony

To hunt a Cyberpony

The Doctor layed down on the pillow to the side of the sheriff’s station, breathing slowly as he sipped from a cup of apple tea Apple Bloom had made him. The farm filly stood by her friend, a nervous smile on her face as her eyes darted from the time colt to the metal contraption that he had called a Cy-boar mane. The thing was still as the night air, even after The Doctor had used his Sonic Screwdriver on it. He said there was some timey wimey stuff on it, at least that’s what Apple Bloom called it. The Doctor had used some big word that even Braeburn didn’t understand, but that was normal for The Doctor.

“Are you ok now?” Apple Bloom asked the brown colt, kneeling down next to him.

The Doctor nodded, “I’ll be fine... Equestria, on the other hand... hoof... might not be.” The time colt stood and walked over to the bars on the jail cell, his eyes locked on the Cyberman in the cage.

“What are these things Doc?” Braeburn asked, breaking his silence as he walked out from behind the desk he was standing by.

“In my world,” The Doctor began, “they where called Cybermen. Here... Well, I guess they should be called Cyberponies. They’re robots, walking suits of armor, with the brains of a pony inside them.”

“Wait,” the deputy pony interrupted, “ your world? You mean...”

“No use hiddin’ it now, huh?” Apple Bloom asked The Doctor, which the colt nodded in agreement, “The Doctor’s a time traveling alien from another planet.”

“... Fine, if ya’ll don’t want to tell me the truth you don’t have ta.” Braeburn fumed, “But don’t make up ol’ foal’s tales just to lie ta me, ok?”

“Understood, sorry...” The Doctor apologized, “The truth is, I’m an agent for Princess Celestia. I investigate strange things like this all the time, and we’ve made up the alien story to keep ponies off our trail.”

“Ah... Now that makes sense.” the deputy closed his eyes and nodded, keeping The Doctor and Apple Bloom’s wink unseen. “So, what where you sayin’ about these... Cyberponies?”

“Yes, well,” The Doctor paused to find his train of thought, “right! Well, the Cyberponies have their minds rewritten, their emotions deleted, and... They’re made to follow one basic thought that’s programmed into their heads.”

“Which is?”

“Delete!” called the electronic voice of the Cyberpony on the floor of the jail cell, “Delete and assimilate!” The robotic pony stood and glared at its captors, the sound of the creature’s gears whirling filled the room.

“Oh, you’re awake now?” The Doctor asked, not a hint of surprise in his voice. Apple Bloom and Braeburn stood behind the time colt, Braeburn ready to charge at the metal beast at anytime.

“Affirmative. Who are you?” The Cyberpony asked, cocking its head to the side in mock confusion.

“Oh come now, it hasn’t been that long has it?” the time colt asked, “You should recognize me, even with all this extra hair. Funny thing about ponies here, their coats are extremely soft. It’s like silk, and it’s just amazing how they can hold things in their hooves. Their hooves!”

“Scanning... Searching memories...” The metal monster stood for a few moments, then took a few steps back, “Analysis complete, subject is The Doctor.”

“That’s it.” The Doctor said, his companions still behind him. “Now, I want some information.”

“All information is classified, as ordered from the Cyber Queen.”

“Cyber Queen? Well that’s new, what happened to the last Cyber Leader?” The Doctor asked.

“Classified, as ordered by the Cyber Queen.” The machine repeated.

“Well, that’s just not nice,” the brown colt walked over to the desk and picked his Sonic Screwdriver up with his teeth, “why don’t we just see if we can fix that.” He said, but since the Screwdriver was in his mouth it sounded more like, “Why dn we jst thee if we ca fix tha?” The Doctor pressed a button on the Screwdriver, setting it off as he had done hundreds of times before. This time, however, it resulted in the Cyberpony behind the cage to scream out and shake.

“D...Doctor...” Apple Bloom looked over at her friend, her eyes wide with fear.

“Don’t worry Apple Bloom, I’m just over-riding his programming!” The Doctor yelled from between his clenched teeth, “It’s only going to hurt him for a little while!” Then, just as he had predicted, the Cyberpony’s shuttering stopped and it stood as resolute as a statue. “Now then... Let’s try this again. What happened to the last Cyber Leader?”

“Cyber Leader 60440,” the metal monster replied, “was destroyed as a result of trans-dimensional travel.”

“So he couldn’t stand the movement between the different time vortexes...” The Doctor pondered, a hoof to his chin.

“Affirmative.” the Cyberpony responded.

“Now, who is this Cyber Queen?”

“The Cyber Queen is the newly crowned leader of the Cybermen,” the cyborg pony replied, “her function is simple, the fulfillment of our mission on this strange planet.”

“And what is that mission?” The Doctor asked, his eyes taking on a completely serious look that Apple Bloom had only seen a few times in her friendship with the strange colt with the blue box. Both times had been when facing threats to Equestria, and the farm filly knew that it meant something bad was going to happen.

“The mission of the Cybermen on the planet dubbed Equestria is the assimilation of the entire population of sentient being on the planet,” The Cyberpony’s gears whirled as it recalled all the information from the once pony brain inside its head, “and the capture of the most powerful weapons of the planet, items known as The Elements of Harmony. With these weapons, as well as the entire population of the following: ponies, unicorns, pegasi, griffons, dragons, and alicorns; the Cybermen will move on to the next planet in this universe and repeat the process. Then, we shall find and assimilate the greatest enemy of the Cybermen, The Doctor.”

The Doctor stumbled back, a looks of fear mixing with hatred crossed his face, “This whole plan... Is so you have an army that can pull me into your ranks?”

“Affirmative, once the Cybermen have The Doctor, the universe will bow down and join the many who have already been assimilated...” Suddenly, the screech of the Sonic Screwdriver filled the room, piercing the Cyberpony’s mind. It screamed out a cry that no pony could make2 or even dream of making. Braeburn shielded Apple Bloom’s eyes as the cry of the Cyberpony filled his ears, the deputy knew what The Doctor was doing. The yellow colt’s eyes never left the scene as he watched the strange brown colt put the once normal Cyberpony out of its misery. All Braeburn could hear over the heart breaking cries was the sound of The Doctor’s voice as he apologized over and over, to whatever was left of the poor colt of mare inside that metal shell.

***

The Cyberpony’s cries filled the air, and the windows of Appleloosa where filled with candle light. As a group of grumpy and scared colts, mares, fillies, and foals trotted to the jail house, another sound filled the night sky. The sound of what seemed like a thousand hooves thundering through the plains, but in reality it was a heard of buffalo lead by Chief Thunderhooves.

“Braeburn!” the buffalo chief called out at the top of his lungs. When the peace between the two species was finalized, Braeburn was chosen to be the liason between the buffalo and the ponies of Appleloosa. In other words, when the buffalo seeked help from the town, they went to Braeburn first.

“I’m here Chief.” Braeburn said as he rushed out of the sheriff’s station.

“Braeburn, have you seen Little Strongheart? She has disappeared, and I fear that if she is not with you then she has fallen victim to the cloaked ones.” Chief Thunderhooves said, panting as he tried to catch his breath.

“Lil’ Strongheart’s missing?!” Braeburn yelled, his eyes filled with worry, “Chief... I think that... Those things may have taken her.”

“That’s all I needed to hear!” a voice called from the back of the crowd, just as The Doctor and Apple Bloom walked outside. To The Doctor’s displeasure, a familiar unicorn in dark armor made his way thought the group. General Stormbreaker smiled as his good eye caught sight of the strange brown colt. “Ladies and gentle-colts, I am General Stormbreaker of the Royal Canterlot Guard, Torchwhoof devision...” he paused as the confused townsponies locked their eyes on him, “I’m here to tell you all that the Royal Guard is taking over this investigation, and that no colt,” the general’s eyes moved over to The Doctor, “shall interfear until it is a closed case.”

(Part 4) Facts, Figures, and Failures.

Facts, Figures, and Failures

The Doctor yawed as he sat in the small caravan that served as the mobile head quarters of Torchwhoof. The outside of the wooden wagon had been very plain, nothing too note worthy; however, the inside was amazingly decorated. The windows where covered in large, dark blue curtains that blocked anypony from the outside’s view, the door had a variety of bolts and locks on it (including an enchantment that General Stormbreaker himself put on it.), not to mention the couches and pillows the various pony guards sat and layed on where as fluffy as a marshmallow. Soon though, the time colt’s eyes where brought back to the unicorn in front of him.

Stormbreaker couldn’t believe his luck. Not only had The Doctor lead him right to trouble, but he was now in full right to interrogate this strange pony for information. The only thing that would’ve made his moment sweeter for the veteran guardsman would’ve been if Princess Celestia herself handed him a metal of valor. “Now,” the general began, “From what you’ve told me so far, we arn’t dealing with an Equestrian threat at all, but a threat from your own world.”

The Doctor nodded, it had taken very little encouragement from the time pony to convince Stormbreaker that The Doctor was from another planet... Another dimension to be exact. The time colt could only surmise that the princesses had told all the members of Torchwhoof this. The Doctor couldn’t help but chuckle in his head, thinking of how ironic this was.

“You haven’t told me what exactly we’re dealing with though, Doctor.” the unicorn tapped his hoof impatiently, “I’d like to know what these... Cyberponies, as you call them, are. What can they do? Are they always hostile? Is there any way we can negotiate with them?” General Stormbreaker waited for a response, but the brown pony across from him remained silent, just as he had from the past hour. The general slammed his front hooves on the table they where sitting at, papers flying into the air and floating down like leaves from a tree. “Luna dammit! Tell me what we’re dealing with you son of a mule!”

“There’s no need to use that kind of language General,” The Doctor sat calmly, as if this conversation was boring him, “If you let me go and leave, I’ll deal with all of this and you can give your full report to Celestia...” A quick smack from Stormbreaker interrupted the Doctor’s train of thought, the sound of a hoof hitting somepony’s cheek echoed through the caravan.

“You will address the princesses by their full title, Doctor.” Stormbreaker glared at the pony he had just hit, “You know, it’s ponies like you that make me sick to my stomach. You think that just because you’ve met royalty, you know them. I don’t care if you’re an acquaintance of Princess Celestia’s top student, I don’t even care about that little 'incident’ in Canterlot, you are not royalty so you DO NOT act like you’re better.”

The time colt spat a bit of blood from his mouth, “I never said I was.” He knew Stormbreaker’s type: aggressive, angry, and a pony that everyone respected just from his past. However, much like the general himself, The Doctor didn’t care who or what Stormbreaker thought he was. All the time pony knew was that if he didn’t deal with the Cyberponies soon, they would have enough foot solders to march on Canterlot... Maybe even all of Equestria. “I’m going to tell you one more time Stormbreaker... I will deal with the Cyberponies. You need to head back to Canterlot,t and tell Princess Celestia that I’m here and dealing with the situation.”

Stormbreaker gritted his teeth, this pony was as stubborn as his brother. Then again, this ‘Doctor’ pony seemed to have gained the respect of both princesses almost over night. Stormbreaker’s horn glowed with a violet-red aura, which then enveloped a file on the table. The file on The Doctor was very small compared to the files of outlaw ponies he had seen in the past; however, it held all that Torchwhoof and the royal guard knew about the strange pony from another world:

Subject: The Doctor

Pictured with Element Bearers Fluttershy and Rarity.

Alias: N/A
Mane: Brown
Coat:Light-Brown
Cutie Mark: An hourglass (suggests a talent having to do with time/time travel/clock making)
Species: Earth Pony
Birth place: N/A
Age: N/A
Children:N/A
Siblings: N/A
Allies: Derpy Hooves (see file marked Derpy Hooves)
- Apple Family(see file marked Sweet Apple): Applejack (see file marked E.O.H.[note: file can only be accessed with permission from Princess Celestia or Luna]), Big Macintosh, Granny Smith Apple, Apple Bloom (see file marked C.M.C.)
-Twilight Sparkle (see file marked E.O.H. [note: file can only be accessed with permission from Princess Celestia or Luna])
-Other bearers of the Elements of Harmony (see file marked E.O.H [note: file can only be accessed with permission from Princess Celestia or Luna])
Enemies: N/A
Additional information: All cases involving the subject known as The Doctor must be reported to Princess Celestia immediately.

“Damned...” The general cursed under his breath. He knew that this strange pony in front of him was right now. It was strange though, Stormbreaker must’ve read that file over one hundred times since being transfered to the head of this new division, but he had never seen anything in the additional information category... unless. The white unicorn glared at The Doctor, “You changed this file... Didn’t you?”

The Doctor smiled and leaned back a bit, “Well now, what ever gave you that idea.”

***

“After that, your majesty,” General Stormbreaker said as he bowed to his matriarch. “My unit left Appleoosa in the... capable hooves of The Doctor.”

Princess Celestia nodded at the last word, by her side was her starry haired sister. The two looked at each other, exchanging glances as if they where having a full conversation in some secret language that only they knew. “Thank you General... After the disturbance we had this afternoon, it is good to hear some good news. You are dismissed.”

“Thank you, your majesty.” Stormbreaker bowed and turned to walk away. In the military unicorn’s mind, however, his thoughts where clouded by hatred. Hatred of being beaten by what he considered cheating, and by some... alien of all ponies! As he exited the throne room and made his usual turn down the hall, the general looked over to the small town of Ponyville just miles from the royal city. “You won this round Doctor... But now that I know what you are, what you can do, I know that I will beat you at your own game.” The unicorn smiled as he looked into the sky, a smile that would’ve made the most innocent of fillies run, “And then... I’ll give you to my true ruler.”

***

Author's Note: If you guys want me to make more Torchwhoof files, just ask and I'll put them in a bonus chapter. Also, the incident that Princess Celestia mentioned near the end happened in my side story Discord in Time!. If you want to check it out, click the link.

Also, thanks for being patent guys.

(Part 5) The Medicine Pony and The Grey Queen

The Medicine Man and The Grey Queen

The Doctor watched as the Torchwhoof caravan made its way out of Appleloosa, dust flying into the hot night air. The time colt couldn’t help but feel proud of his little stunt, not only did it mean that he survived the encounter with these Cyberponies, but it hopefully meant that the rest of Appleloosa and Equestria did too. He made his way back to the jail/sheriff office, his eyes still adjusting to the dark of Luna’s night... Then he heard the laughter. It was a strange sort of thing to hear at night in Equestria, the laughter of a filly at about two in the morning, but what made it even more odd was that it seemed familiar. The Doctor looked around the nearly barren landscape, but the buildings of the town itself where the only things to be seen. Suddenly, the sound of hundreds of hoof beats filled the air once more, and The Doctor turned to see the buffalo herd heading straight for him.

Chief Thunderhooves stopped just inches in front of the time colt, with his herd following his lead and halting inches from their leader. Only the hoof beats of Braeburn and Apple Bloom still thundered through the night sky as they charged toward their friend. “Doctor!” Apple Bloom called out, “the buffalo say they think they know where the Cyberponies are!”

“What?” The Doctor asked, a look of surprise on his face, “Is this true Chief?”

Thunderhooves nodded, “Yes Medicine Man, we have seen the cloaked ones many times during the last few nights, and they always seem to head towards the same place... Dodge Junction.”

“But ain’t that where cousin AJ went after the Canterlot Rodeo?” Braeburn asked, “Why would those metal things travel all that way, just to take ponies and buffalo from here?” Before Braeburn could get an answer, another thought sprang to his head. “That means... Lil’ Strongheart...” The deputy pony turned and ran to the general store, his mind set on buying the tickets to save his friend’s life. Before The Doctor could stop the stetson wearing pony, the Chief cleared his throat.

“There is something else that we must discuss, Healer.” The buffalo began, “Our elder foresaw this all, including your arrival. He spoke of a strange pony that would carry a magic stick, who would save these lands from certain destruction from the steel parasites. If you truly are this pony, the elder would wish to speak with you.”

The Doctor nodded and turned to Apple Bloom, “I need you to go with Braeburn to Dodge Junction. Tell him that I can’t make it, but to tell me anything that he finds there.”

“Awwww, but Doc-”

“Shush Apple Bloom. This is something only you can do, ok? If you don’t got with Braeburn, he might not find what we’re looking for.”

“But how do you know that I know what we’re looking for?” the filly asked, still pouting at her friend.

“You’re smart Apple Bloom, and you’ve seen the things that I’ve had to deal with here.” The Doctor smiled reassuringly at the farm filly, “If anyone can find something strange going on, it’s you.”

“Ok...” Apple Bloom’s voice was still filled with doubt. Big Mac and Applejack had told her something similar to this hundreds of times, but she never expected her friend, the friend she had helped save all of Equestria with, to tell her this. Maybe it’s for my own good, she thought, Maybe he’s tryin’ to protect me... I just can’t shake the feeling that he’s just brushing me off like AJ does when she’s buckin’ apples. Still, the red maned filly trotted after her older cousin as the voice of The Doctor reverberated in her mind ‘go with Braeburn’.

***

The herd sailed through the desert like a ship on the high seas, The Doctor at the head with Chief Thunderhooves. The time colt couldn’t help but shake the feeling he had had at the Mayor’s office in Ponyville, it just didn’t make sense. These ponies, he thought, they’re years behind humans in some forms of technology, yet they have all this magic surrounding them. Magic, which they didn’t need to use to get pictures of me, which is something humans can barely do at all. Humans are lucky just to see me once in their lifetime, but these ponies... I’m friends with a good amount of them! The Doctor sighed as he kept running, I mean, yeah, it’s nice here... But something just doesn’t feel right. Like someone’s watching me... waiting for... something...

“Healer!” Chief Thunderhooves bellowed over the stomp of his herd’s hoof beats, “We are nearly at our village!”

The Doctor shook his head clear, placing the strange thoughts in the back of his mind as he saw the teepees. Soon, the buffalo village became clearer in the deep, starry background, and the fire in the middle of the circle of tents was the obvious stopping point. Unfortunately, the buffalo didn’t agree, pushing on past the fire and knocking The Doctor onto his back before they finally stopped. A few laughs came from the herd, some of the children giggled and asked their parents ‘Who’s that silly pony?’, but soon they were all silent as the soft hooves of another buffalo joined them.

This buffalo looked ancient, his coat seemed speckled with a fresh snow that shook as he trotted towards the time colt. The Doctor soon sat up and saw the elder fully. The elder buffalo wore no head dress, much like the other younger buffalo, but his horns were decorated with carved markings and two eagle feathers. “Hello strange one,” the elder said as he took a seat at the fire, “I have been expecting you... My name is Endlessgaze, and your visit here is no coincidence.”

The Doctor walked up to the fire, sitting across from the elder buffalo before he spoke. “What do you mean?”

“Weeks ago, when the moon was full,” Endlessgaze began, “I slept in this very spot and was given a vision from the ones who rule all.”

“The princesses?”

The elder buffalo laughed, it was dry but kindly at the same time. “Oh, you ponies. Thinking that there are beings here that rule all... No, I speak of the two at war, Order and Chaos. They both see that you are here, and are hoping to return to your rightful place and keep the balance until then.” Endlessgaze paused, possibly waiting for the time colt to respond, then began again, “My vision was of a kingdom of strange beings that ate ponies and buffalo alike, they dressed in cloaks but wore suits of metal that would never come off. It also showed a brown colt, fearless yet full of fear, that would challenge these creatures and defeat them with the aid of his allies. I believe that you are...” The buffalo paused again, his eyes going white as the moon itself.

“Endlessgaze?” The Doctor stood and began to walk around the fire, and closer to the elder. Suddenly, the elder buffalo’s body was lifted into the air as his empty eyes seemed to focus on the time colt.

“Hello Doctor, it’s nice to finally see you.” Endlessgaze’s lips moved, but a different voice radiated from them... The voice of a young filly, “Then again, we’ve met before, back if the forest of the forlorn.”

“You!” The time colt yelled, “You’re the being that possessed Zecora in the Everfree Forest!”

“Of what you know, that is correct. However, time right now is indirect.” the young voice said through the elder, “I must tell you of your task, but this aid will be my last. For the task at hoof you see, you must have an army unseen, but fear not gentle friend, for your allies have that at hand. Though de beware the Grey Queen, for her gambit is too unseen.” The elder shut his eyes and slowly began to float down to the dust and sand below, and while the buffalo tended to his needs, The Doctor turned and made his way back to the town. He needed to get to Dodge Junction, and fast.

***

Little Strongheart opened her eyes, then quickly wished she hadn’t. The young buffalo shivered as her eyes fell onto the masses of metal ponies surrounding her, their cold, black eyes seemed to stare deep into her soul. Soon, the sound of metal hitting metal filled the room as a tall, silver alicorn entered the room. Her wings were long and beautiful, but much like the other Cyberponies her eyes were dark and lifeless.

The alicorn machine turned to face Little Strongheart, “You poor, poor dear.” Its voice was soothing, but metallic like its shell. “You must be scared to death... Good. You need to be scared for this.” Soon, Strongheart heard something buzzing and looked up to see a drill slowly advancing down, the sound of the whirling metal sending shivers down her spine. Soon, the Cyber Queen spoke once more, this time in the voice her subjects used as well. “We shall delete the weakness, delete the emotions, delete the negative, and leave only the collective. We shall assimilate... We shall rule.”

“Not yet.” A new voice called out, it was deep and obviously not another Cyberpony; however, the drill stopped and all of the steel horses and their queen turned to the origin of the voice. It was somepony in a long cloak made of what seemed like sown together patches of other cloaks. Under the hood, Little Strongheart could barely make out a horn. “This one can wait, because you have yet to delete The Doctor!”

The Cyberponies shrunk back in fear of the cloaked pony’s voice, only nodding and running away. The strange pony then turned to Strongheart, “I swear, it is so hard to find good help these days.”

“Who... Who are you?” the young buffalo asked. She could see a flash of white and yellow teeth from under the dark hood as the new pony answered.

“Just somepony that everypony should know...”

Torchwhoof Files: Derpy Hooves and C.M.C.-1 (Apple Bloom)

Subject: Derpy Hooves

(Pictured with room mate Golden Harvest. Note: strange, unexplained phenomena seen in bottom corner of photo)

Alias: Ditzy Doo (maiden name)

Mane: Blonde

Coat: Grey

Cutie Mark: A trail of bubbles (meaning unknown)

Species: Pegasus

Birth place: Manehattan

Age: 25

Children: Dinky Hooves, Sparkler Hooves.

Siblings: None

Allies: The Doctor (See file marked The Doctor [note: file can only be accessed with permission from Princess Celestia or Luna])

-Lyra Heartstrings and Bon-bon Legateau (see files marked Lyra and Bon-bon)

-Twilight Sparkle (See file marked E.O.H. [note: file can only be accessed with permission from Princess Celestia or Luna])

-Golden Harvest (See file marked ‘Carrot Top’)

Enemies: Unknown

Additional Information: Miss Hooves recently went through a divorce in which her two daughters were separated. The father of the two, (name deleted), still allows Sparkler to visit her mother and little sister. However, this may explain possible ‘abandonment issues’ Miss Hooves may have.

***

Subject: Apple Bloom (C.M.C-1)

(Pictured here selling apples)

Alias: None

Mane: Red

Coat: Pale-Yellow

Cutie Mark: None as of yet

Species: Earth Pony

Birth place: Ponyville

Age: 8

Siblings: Applejack [note: file can only be accessed with permission from Princess Celestia or Luna], Big Macintosh

Family: (See file marked Sweet Apple for details) Big Macintosh, Applejack [note: file can only be accessed with permission from Princess Celestia or Luna], Braeburn Apple, Granny Smith, Apple Fritter, Apple Pie, Apple Blossom, Crab Apple, Mr. and Mrs. Orange, etc...

Allies: Scootaloo and Sweetie Belle (see files marked C.M.C. -2 and C.M.C.-3)

-Dinky Hooves (see file marked Derpy Hooves)

-The Doctor (see file marked The Doctor [note: file can only be accessed with permission from Princess Celestia or Luna])

-Zecora (note: information unavailable on subject known as Zecora)

-Snips

-Snails
-Miss Cheerilee

Enemies: Diamond Tiara (see file marked Filthy Rich)

-Silver Spoon (see file marked Bronze Fork)

Additional information: After the peaceful death of her parents (Apple Tart and Appleseed) subject has had very few father figures in her life. This may explain her deep love of her family, as well as the quick friendship of the subject known as The Doctor. It is unknown, as of yet, if she sees The Doctor as a father figure or not; however, it is believed that she does see her brother (Big Macintosh) as both a father and brother.

(Part 6) The Grey and Unseen Armies

The Grey and Unseen Armies

As the train raced toward Dodge Junction, The Doctor’s mind raced as well. Multiple possibilities filled his head: Who was the ‘army unseen’ that Endlessgaze referred to? What were the Cyberponies doing so far from where they were kidnapping ponies? But most of all, the time colt worried about Apple Bloom. She was a strong willed filly, but she had no clue what she was up against. Neither did Braeburn, but at least he was a full grown stallion; Apple Bloom had basically just begun life, and after what happened to...

The Doctor shook his head, trying to wipe it clean like a dry erase board. “No... No, I can’t think of what happened to him.” the brown clot said out loud, “Adric wouldn’t want me mourning him, especially after all this time.” Suddenly, a sharp whistle filled the air, followed by a call from the conductor... Next stop, Dodge Junction.

***

Braeburn ran through the alleyway, Apple Bloom struggling to try and keep up as a wall of shining silver ponies marched closer and closer. As soon as they got off the train, the two Apples were assaulted by the brigade of Cyberponies. The metal monsters fired some sort of magic at them, magic that made the caboose of the train explode into flames when it was hit. All the while, the mechanical ponies said only one word over and over again.

“Delete, delete, delete.” the word echoed from their unmoving mouths, like an old eastern pony monk’s montra. “Delete, delete, delete.” Their constant repeating of the phrase began to wear on the deputy pony’s nerves, and Celestia knows how it was effecting poor little Apple Bloom. Still, the only thing the two could do was run as fast as they could, and as far as they could from the steel sentinels. Braeburn turned, his eyes meeting the dull, empty sockets of their pursuers, but he also saw something that made his heart jump. Apple Bloom, in an attempt to trick the monsters chasing her, had hidden behind a bunch of water barrels; however, as if the creatures could see through the solid wood, a group of three Cyberponies closed in on the farm filly.

“No!” the Appleoosan deputy cried, turning himself around so fast that it kicked up a cloud of dust around him, “Ya’ll leave her alone!” The brave, orange maned pony galloped at the group of armored monsters, his head bared down in an attempt to ram them out of the way. As his skull connected with the cold, hard metal of a Cyberpony’s side, Braeburn realized how much of a bad idea this was. The hit sent him to the ground, dizzy but not unconscious.

“Take them.” one of the metal ponies commanded, “The Doctor will follow if his allies are captured alive. We shall trap him, for the Queen.”

“Not much of a trap if I can hear you talking about it.” a deeply Trottingham-like voice said. The Doctor stepped out of the shadows, his eyes glaring in rage at the group of metal creatures.

“You will come with us.” The lead Cyberpony ordered, “Or they shall be assimilated.” The metal pony pointed his front hoof at the two Apples, Apple Bloom now in full view as one of the Cyberponies held her by the nape of her neck in it’s metal jaw.

“I’ll come with you, but you have to let them go and leave them alone.” The time colt said, “After all, they’re just normal ponies. I’m worth at least ten of their kind, right?”

The Cyber Leader nodded, “Affirmative, release them and apprehend The Doctor.” Soon, the alleyway was empty aside from two ponies, one dizzy and one scared out of her mind.

***

Braeburn and Apple Bloom walked along the main street of Dodge Junction, their bodies tired but their minds working tirelessly in the hope that they could find their friend.

“I just don’t get it...” Apple Bloom said, her eyes still red from the tears she shed during the attack, “It’s not like they could just disappear.”

“I don’t know lil cousin.” Braeburn replied, his voice sounding weak and tired, “We’ve looked all over APP- uh... I mean Dodge Junction, it’s like he disappeared.”

“Just like Applejack disappeared here after the Rodeo last year.”

“Applejack?” a voice called out to the two, and suddenly a red maned mare with a creamy coat stood in front of the two tired ponies. On her flank were three cherries with interlocking stems. “Did one of you say Applejack?”

“Eeeyup...” Braeburn replied, “Do you know her miss?”

“Jubilee, Cherry Jubilee.” the mare said, “Applejack said she had family in Ponyville,” Cherry looked down at the little farm filly in front of her, “Why, you must be Apple Bloom!” Her eyes then moved over to the Stetson wearing colt, “And I’m guessin’ you’re Braeburn, from Appleoosa?”

“That’s right ma’am, say...” the deputy pony pondered for a moment, “You wouldn’t know about any strange happenin’s around here, would you? Like ponies being abducted at night?”

“Oh my... No, but I’d be happy to help ya’ll look for your friend.”

“That’s mighty neighborly of ya Miss Jubilee...” Braeburn said, tipping his hat... When Apple Bloom suddenly jumped up and pulled off the imposter’s wig. Braeburn then tackled the pony to the ground and pinned it. “But we never told ya we were lookin’ for anybody.”

The fake Cherry Jubilee struggled, and her eyes focused on Braeburn with rage. That is, until Apple Bloom pulled the imposter’s eyes out, revealing dull, empty, Cyberpony sockets.

“Now,” Apple Bloom began, “ya’ll better tell us where you took The Doctor.”

“Negative,” the metal pony said, “you shall be deleted. Delete! Delete! De-” The mechanical monster was cut off as it’s head was surrounded by a grey, magical aura and pulled clean off it’s neck. Apple Bloom and braeburn then looked up to see Cherry Jubilee and a white colt in a brown poncho and flat top gambler-style hat on his head. The mysterious colt tipped his hat, revealing an alabaster horn under it.

“Well,” Cherry said as she looked over the destroyed Cyberpony’s body, “I understand ya’ll are lookin’ for their hide out?”

“Yes ma’am!” Apple Bloom yelled out.

The unknown colt then stepped up, his aura illuminating a pocket in his poncho and pulled a business card from it. As it floated in front of Apple Bloom, she and Braeburn looked over it:

Unseen Stallion Bounty Hunting
Colt Easthoof

(Author's Note: It's Doctor Who trivia time! When The Doctor's worrying about Apple Bloom getting hurt, his mind went back to a very dark time in his life. During the original run of Doctor Who (before the hiatus that seemed to cancel the series) the fourth Doctor (Tom Baker, best know for his multi-colored scarf of legend) picked up an adolescent alien genius from a parallel dimension naked Adric. Adric stayed on as a companion of The Doctor, even when the Doctor regenerated for the fifth time (into Peter Davison, know for flipping a coin to make decisions). However, Adric's story does not have a happy ending. During the episode Earthshocker, Adric tries to stop a Cyberman frieghter from crashing into Earth. He doesn't make it, and instead the freighter crashes with him on it... While The Doctor and his other companion watch from the TARDIS, unable to help. This effected The Doctor greatly, and he hasn't had a companion Adric's age since. I hope this clears things up for you guys.)

(Part 7) Hoof Full of Bits (or, The Good, The Bad, and The Mechanical)

Hoof Full of Bits

(Dear reader, I apologize if this seems rushed. The first draft I wrote of this seems to have gotten deleted, and I want to try and wrap up with fic, so that I can start on the next installment of Doctor Whooves.-Mule)

***

The Doctor groaned as his eyes opened slowly, the sounds of grinding gears gnawing at his mind. The time colt turned his head, surveying his surroundings as best he could in the near pitch black room. All around him where Cyberponies, their black, empty eyes staring into his soul as they watched their captive stir from his sleep. Behind a large group of theses monsters was something a little different: a taller metal pony with wings and a horn, and a normal sized pony in a pure black cloak.

“Well... Hello.” The Doctor said, smiling cockily at his enemy, “You must be the Queen Cyberpony.”

“Affirmative,” the tall robotic horse replied, “I am the unit designated as Cyber Leader-QU33n. And you are The Doctor.”

“Yes, very good, now can you say your ABC’s?” The time pony chuckled, but was soon silenced as one of the Cyberpony soldiers hit The Doctor straight in the stomach with their hoof. Slowly, the room was filled with the soft laughter of the cloaked pony, it was a regal laugh but at the same time feminine. The strangest part was that it was familiar to The Doctor, his mind began working hard to try and match the giggle to a face.

“Doctor,” The Cyber Queen began, “you will be the final component in our plans. We shall finally show you the error of your ways. There shall be no individual unit, from now on this world and yours will be peaceful. It shall become one with the great power of the Cybermen.”

“Th...That’s all well and good,” The Doctor said, trying to catch the breath the Cyberpony had knocked out of him, “but I must ask... Why are you taking orders from someone else?”

“Elaborate.” was the only response.

“Well, it’s obvious that the pony next to you hasn’t been assimilated yet. I can still see his or her coat, a lovely sort of white by the way-”

“Thank you.” The cloaked pony said, a smile curling under her hood.

“-So why would you take orders from her? She’s no Cyber Leader, hell, she isn’t even a Cyberpony! There’s only one answer I can think of, and I’m sure it’s one you don’t want to hear.”

“Silence...” The Cyber Queen said, a slight sting in her voice.

“You’re afraid of her, aren’t you?” The time pony continued, ignoring the cyber alicorn’s request, “She’s powerful, much more powerful than even you are! I’m sure she could even cross dimensions if she wanted, and that makes you afraid.”

“Silence!” The Cyber Queen shouted, her front hooves seeming to dig into the ground beneath her.

“And in the end, you learned something after you assimilated your first Equestrian, didn’t you? Just like I learned something when I reprogrammed the Cyberpony Braeburn captured.” The Doctor glared at the Cyber Queen, but a grin stayed glued to his face, “Creatures here are tougher to reprogramme, much more stubborn than humans, right?”

“SILENCE!” The tall mechanical pony arched back her wings, as if she were going to pounce on The Doctor and rip his throat out.

The Doctor then lifted his head and looked out among the crowd of Cyberponies. “Little Strongheart! If you’re out here, Braeburn is still looking for you!”

The Doctor waited, and for the longest time there was nothing. The sound of the wind blowing through the wooden walls of the building they were in filled the air, as if it was the only noise that would ever break the disturbing quiet. Then, suddenly, a regal laugh could be heard echoing through the room, and The Doctor’s eyes focused on the cloaked pony once more.

“You sad little Time Lord.” The figure began, “You truly think that I would leave any seems undone? These poor, pitiful creatures are like lost little puppies with out my orders, and my orders are always to shut up and obey me.” The mysterious pony turned and began to walk to a small control panel, “I don’t know what my master sees in you, he told me you could do anything. I guess even cowards have limitations, huh? Oh well, no harm done, you won’t be harmed... In fact, my orders are to make sure you’re never hurt again.” Her hoof hovered over a large red button, a smile still plastered on her mouth. “A little assimilation should make that an ea-”

“B...Braeburn?” a mechanical voice said through the cloaked pony’s speech. The mare turned toward the crowd of monster machines.

“Who said that?” she asked, her teeth grinding under her cloak, “... I asked who the buck said that?!”

Suddenly, all the Cyberponies turned, their hoof beats sounding like the march of a cavalry. Then, all at once, they spoke. “I did!”

Even though The Doctor couldn’t see the cloaked pony’s eyes, he knew they were wide with fear and confusion. “I told you, ponies are tougher. I guess that goes for buffalo too.” The cloaked figure turned towards a wall as a bright magical beam blasted it, blinding The Doctor temporarily. The time colt could hear the distinct sound of hooves galloping across dirt; however, the hoof beats stopped suddenly as a small voice called out a single word.

“Doctor!” Apple Bloom ran up to her friend and hugged him tight, they had found him.

***

“What do you mean you knew we were comin’?” Apple Bloom asked, a confused look on her face. “It was Mr.Easthoof who knew were in the wide wide world of Equestria you where!”

Braeburn nodded in agreement, he couldn’t help but think The Doctor was talking out of his plot when he said that. He turned his head and smiled at Little Strongheart, and his mate smiled back. It had taken a long time, but a letter The Doctor had written to Ponyville finally got through. After a day or two, Applejack and her friends finally got to Appleloosa, along with a team of unicorns lead by Miss Twilight Sparkle.

It seemed that the Cyberpony-ization was pretty weak after all, and unicorn magic was able to reverse the process. A slight frown crossed Braeburn’s lips as he thought of the two ponies that lost their lives, the one killed by The Doctor and East hoof, before they could get this information. “Poor colts...” the deputy pony said out loud. Strongheart put her head on his neck, trying to comfort her coltfriend. The deputy smiled once more, his eyes closed as he remembered their deaths were not in vain.

Slowly, the 1:25 to Ponyville pulled up the the station, each of its passengers climbing aboard. As the train left the station, The Doctor looked back on the small oasis in the wasteland and frowned, his mind buzzing with questions. Who was that cloaked mare? Why did she seems so familiar? And, the one in the forefront of the time colt’s mind, who was her master?

To be concluded...

Epilogue

Applejack raised her mug of cider as she ended her toast to The Doctor, her long blonde mane swayed as she shook her head at the sight of Pinkie Pie chugging down another three helpings of her family’s home brew. The farm pony’s eyes drifted across the room, taking in the sight of all her friends before stopping on the barn door. Exiting the giant room was the brown colt she had just finished toasting, and Applejack wasn’t going to stand for her guest leaving without so much as a good bye. She galloped after him, passing the time colt and skidding to a stop right in his path. “Where do ya think you’re goin’?”

“Well... I was just heading home, it’s a bit late.” The Doctor explained, smiling a bit too nonchalantly for AJ’s taste.

“Ah huh,” Applejack said,” and after you try to lie to the Bearer of the Element of Honesty, what exactly where ya’ll goin’ to do at home?”

The Doctor sighed, knowing it was a bad idea to try to lie to any of Twilight’s friends. “I was... Going to leave... For good.”

The orange mare stood her ground, her eyes softening as she smiled. “Doc, I gotta tell you something. Ever since you came here, Apple Bloom’s been tryin’ ta get her Cutie Mark more and more. You wana know why?”

The time pony paused, “Because... She wants it now?”

Applejack laughed, then shook her head. “No, she wants to be seen as more mature. She wants to be seen as more of an adult, and she wants that because you treat her like she’s already got it. Sure, me and Big Mac try to give her more responsibility, but she’s our baby sister... It’s hard to see her as anything but that.” AJ took a few steps towards the barn, “I thought you might like ta know that before you head off to your other world.” Then, the cowpony stepped back into the party, laughing as Pinkie began a bright, cheery song about some holiday she’d never heard of. Her thoughts were still on The Doctor, until she noticed one of her guests seemed to be missing. A guest that most ponies would never miss at a party like this.

***

The cloaked pony bowed before the shadow covered thrown, the destroyed, former fortress of Nightmare Moon seemed to crumble more and more as she waited for her master to speak. Her eyes gazed up at the creature sitting in the large chair, its hooves clicking on the arm of it. “Once again,” she began, “I apologize my king. You were right to warn me of the time colt being brilliant, and I was stupid enough to think I had won. I throw myself at your mercy, my master.”

The figure in the throne looked over his servant, a strong creature with uncanny beauty. It couldn’t help but laugh coldly at her attempts to appease him. “You truly are pathetic, little mare. You think I didn’t account for you being too thick skulled to heed my orders, or that I wouldn’t have a secondary plan? How naive...” The creature looked over at the large doorway to his right, just as General Stormbreaker marched in. “Good, my other puppet is here too. Is the Rani in our custody?”

“Yes, my master.” the general said with a bow.

“Brilliant. All we have to do now is wait and watch...”

***

As The Doctor walked into his beautiful blue box, he smiled at the warmth of the control panel. “Hello sexy, did you miss me?”

“Doctor?” a voice from inside the TARDIS said, quietly.

“Well,” the time colt said, a little bit of confusion in his eyes, “I didn’t know I programmed a voice applicator... Sounds a bit like...”

“Doctor,” Derpy said, stepping out of the hallway, “where you talking to yourself?”

“... Maybe.” The Doctor replied.

Derpy couldn’t help but blush as she walked toward her friend, her head laying across the back of his neck in a hug. “I... I missed you.”

“Derpy...” The Doctor smiled, blushing with her before backing away, “Wh... Where’s Dinky?”

“She’s at her father’s in Canterlot for the weekend.” she replied, but before The Doctor could ask why the grey mailmare never told him she was married, the pegasus kissed him on the cheek lightly, “I gotta get going, bye.” The brown colt stood there, his eyes on the control panel as he waited for the shock to blow off... Then Derpy peeked back into the TARDIS, “River send a message saying hello by the way.”

“Ah, that explains it.” the colt replied as Derpy giggled. Once he was sure she was gone, The Doctor stepped up the one of his monitors and gasped. “She... She’s at full power... She’s at full power!!!” The time colt began to dance with joy, his smile threatening to break his cheek bones, and as he reached for the handle that would activate the quantum flux-drive... He stopped. The Doctor looked back at the door of the TARDIS, smiling as he remembered that past few months. His hoof left the lever on the console as he sighed, “Maybe just a little longer...”

To be continued in... JNDJASFNGDANOJSGNDSJGN

~~Signal Interrupted... Transferring... For English press one, para Espangol prima dos...~~
Hello? Hello, is this thing on? Yes?... Good. *sounds of a mare clearing her throat*.
Hello strange and ugly humans! It is I, The Great and Powerful Trixie, here to tell you that Trixie will be the head liner in the next Doctor Whooves fan fiction. Do not expect a convoluted plot about robots or time ponies, no this next fic will be all about me, Trixie! If you don't like it, you can lump it.

Expect daring battles, culminating in what every one of you strange, two legged creatures have been asking for, The Great and Powerful Trixie versus twilight sparkle. Oh, and there's something about a cloaked pony here and that stuck up egotist, Rarity, but that's not important! What is imporant is I, The Great and Powerful Trixie! *sounds of fireworks going off in the background*.

So tune in, because Trixie will be appearing in Doctor Whooves T.G.A.P. Trixie: Battle Royal!