Doctor Whoof and the Elements of Discord

by Trickquestion

Rating: teen
Tags: Adventure, Crossover, My Little Pony: Friendship is Magic, Dark, Doctor Whooves, Original Character
Length: 16039

An enemy of the Doctor has risen, and wields a power that could destroy Equestria

A mysterious shadow of the past and future is haunting the Doctor, using ponies as puppets to menace the time pony and impose its will upon Equestria. Weilding the lost chaos magic of Discord in six Elements of evil, will the Mane Six be able to defeat this new evil and its minions? Or will a dark and endless night cover the land forever? The story may be a touch confusing for non-Doctor Who fans, but I've put story notes in a points where the references get a little thick, but not where they'll spoil dramatic tension. A great deal of death occurs, but nothing of an overly gory sort.

Published 2012-01-15 04:22:58 UTC
Last updated 2012-01-28 02:23:39 UTC

An Unearthly Pony

Chapter 1

It's a bright and sunny day in Ponyville, Celestia's sun illuminating the land from its perch up in the sky. It was a perfect day, the kind on which it seemed nothing could go wrong.

Which, naturally, meant something was about to go horribly wrong.

Unaware of the impending crisis, just like everypony else, the pegasus pony known as Derpy Hooves went about her business, currently purchasing muffins at the grocery store. After pushing her muffin-laden cart to the check out stand, the wonky eyed pony did a double take when she saw who was mareing the cash register.

"Doctor? Is that you?" The mail mare asked. "It can be a little hard to tell sometimes..." she added sheepishly.

"No Derpy, it really is me." Replied the chestnut Earth pony with the hourglass cutie mark behind the counter. Known only to the residents of Ponyville as Doctor Whoof, the stallion was somewhat of a mystery, always poping in and out of the blue in an unpredictable way. Only Derpy and her two daughters knew the truth: The Doctor was an alien Time Pony, who traveled across time and space fighting aliens and monsters.

Derpy (and later her husband, Neighy) had joined the Doctor on his adventures, during which they adopted Sparkler, who had been orphaned by the Daleks, and gave birth to Dinky, who had almost been kidnapped by the Silence. However, after Neighy was killed by Sontarans (in the same attack that left Derpy with her trademark wonky eyes) the mare and her children returned to Equestria, to mourn and, eventually, move on with their lives.

It had been almost four years since then, and Derpy, though she missed her husband every day, has largely managed to move on, consoling herself with the love she recived from her daughters. She did not hold it against the Doctor, for if it hadn't been for him, she and the rest of her family would probably have died as well.

"I'm in the area tracking some Cyber-Stallions. I'm working in a shop while I keep my eyes out. They even gave me a little nametag, so I don't forget who I am!" The Doctor explained while motioning to his nametag, which proudly read "The Doctor". "That has actually happened once or twice."

"Well, it was nice to see you Doctor. Stop on by sometimes and we can reminisce." Derpy said as she paid for the muffins and headed out the door.

"Say hello to Dinky and Sparkler for me!" Doctor Whoof called out.

Saddlebags full of muffins, Derpy trotted towards home, but she stopped suddenly after the sight of a muffin atop a roof entered her eyes. Ironically, had her eyes not been malformed, she wouldn't have noticed it. "FREE MUFFIN!" Derpy exclaimed as she took to the air. Though a resonably intelligent mare, Derpy loses control when confronted with muffins, for she had a great love of the baked good, relating back to when Neighy would take her on dates at the local muffin outlet. During her adventures with the Doctor, she would frequently offer them to whatever manner of alien they would be dealing with that week. Her love of the goods had become slightly obsessive since her husband's death.

After reaching roof level, Derpy ate it in one bite before sighting another one at ground level. Swooping down to consume it too, Derpy saw another, then another, until the path of baked goods lead her to the end of a dark alley. Oblivious to her surroundings, yet realising this would be her last muffin until she got home, Derpy took her time savoring the last one, unaware she was being watched.

"There she is!" An ethereal voice spoke in the mind of a unicorn viewing an unsuspecting Derpy from the dark. The male voice was cold and commanding. "Use the device, just as I have instructed you."

A steel black, cigar shaped object enshrouded in the light pink glow of a unicorn spell moved around in the air, before taking aim at Derpy. After a few seconds of the air remaining still, the voice returned.

"You must not hesitate now! This shall be the begining of our revenge! This is the first step in making the Doctor, and that petulant Twilight Sparkle and her friends, pay for what they have done!"

The glowing intensified as a mechanical humming filled the air. Derpy turned around, her mouth opening to scream, but she was silenced in a flash of light before the day's peace could be disturbed.

A few hours later, Doctor Whoof was placing a broom back in a closet at the groccery store. It was closing time at the Doctor's temporary place of employment, and it was his night to sweep up. Cheerfully humming the Winter Wrap Up song as if he heard it yesterday (which, considering his ability to travel time, he very well might have) he tidied up his station and left the building.

Only a few feet away from the store, Doctor Whoof stopped when he heard his name called. "Hey Doc!" cried his manager. "Some unicorn dropped this off earlier." He informed while dropping a small package, wrapped up in TARDIS blue paper with a red bow on top. "She was pretty cute looking too, you sly dog you." he added while nugging the Doctor in a suggestive manner before walking away.

The Doctor, however, was too astonished to react (with embarrassment, as it would have been) to the manager's allegations. The color of the box matched that of his Time Machine, the TARDIS, perfectly. Whoever sent this knew who he was. Wary but curious, Doctor Whoof slowly undid the wrapping.

He then gasped in horror, recognition, and fear when he saw what was inside.

Within the box, beneath the blue wrapping, was the shrunken, tissue compressed body of Derpy Hooves.

He was returning.

Survival

Chapter 2

Unaware of the chaos that was hanging right over everypony's head, the prize pupil of Princess Celestia, Twilight Sparkle, sat in her library home enjoying a book. This was to change, suddenly and terribly, as the strangest stallion she would ever meet burst through the door, disturbing her time of ordered calm.

Doctor Whoof, displaying his typical lack of regard for mortal tact, burst through the door and instantly began ruffling through the purple unicorn's things. "Alright, I'm going to need a squad of royal guards on standby, complete maps of the Everfree forest and a..." The Doctor trailed off when he read the title of a book that had been knocked to the floor in his haste. "13 Easy Spells to Better Manage Your Time?" He paused for a moment. "Well, good to see my book is still in circulation."

Twilight, who had been staring at the strange intruder with a blank stare until now, finally managed to summon words once her book expert instincts kicked in. "Your book? This was written over a hundred years ago." She stated while pulling the tome away with her magic. "And what are you doing in my house? Who are you?"

"I'm the Doctor!" Whoof responded perkily. "I already know you, Twilight Sparkle, but I don't think you've meet me yet." His expression then became grim and serious. "There has been a terrible murder, Twilight, the first of many. And I'll need you and your friends to help stop it."

Not too long after the Doctor's grave announcement, the holders of the Elements of Harmony had assembled inside Twilight's home. "Now, as you all know, Princess Luna was transformed into Nightmare Moon by loneliness and jealousy." The Doctor explained, pacing back and forth before the six. "But there's more to the story then that. Luna's own feelings were altered, amplified by a psychic parasite, one that I am familiar with."

Rainbow Dash was not going to put up with this though. "Alright, listen up weird guy, I've had just about enough of your rambling! How do we know any of this is even true?"

"Ease up Dash. He's show me some papers indicating he's a representative of the Princess. Plus, he knows details about Nightmare Moon only the Princess or us could know." Twilight replied calmingly. "Please, continue Doctor."

"Thank you Twilight." The Doctor stated. "After his last encounter with me, this parasite sought a weapon he could defeat me with. What he found were The Elements of Discord." He explained omminously.

"What, how is that meanie beanie fo-fiene Discord involved in this?" Asked Pinkie Pie with an inquisitive look on her face.

"After Discord's first defeat, remenants of his magic were collected and forged into tools of evil, by Ponies that sought to obtain power at any cost." The Doctor continued. "After his last defeat, my foe collected the Elements, and, using his mental powers, forcefully combined them with Nightmare Moon. It was his intent to use her as his champion. It backfired, though, and he became a prisoner within Nightmare's mind. When you destroyed her, the innocent Luna was freed, but his evil was left within the remains of the Nightmare, hopefully to dust forever in the Everfree forest. But now I fear someone intends to free him..."

"Then why we all lazing around here?" Applejack spoke up abruptly. "Giddy up everypony! We need to get to Everfree Castle, pronto!"

As the Element bearers and The Doctor left Ponyville, their foe was already half way to the castle. Arriving far ahead of her adversaries, the unicorn who killed Derpy survayed the room where Nightmare Moon had been transformed back into Princess Luna. Fragments of the evil mare's armor still lay upon the floor. Leaving the shadows and stepping into the torch light to reveal her identity as...

"Now Trixie, begin the ritual! Once I am reborn, I shall make you as great and powerful as you wish." The voice in the washed up magican's head commanded. Slightly overwhelmed by how deep in she was getting, Trixie nodded her head and got to work, dropping the saddlebags that had weighed down her flank upon the floor.

She began by gathering the armor fragments and duct tapping them together in a vagely tower-ish shape. Then, complex figures were precisly drawn on the floor in an multi-layered pattern around the hastily made statue. Elixers of life (which required some careful theft to produce) were poured about, and used to moisten the crude monument with a rag. Four drums were scattered about the room. Special candels were burned, and mystic runes were carved.

Finally, after a great deal of preparation, the ritual was ready.

A chill briefly seized Trixie, who paused fora moment, wondering if she could still back out. When the voice appeared in her head two months ago, Trixie had begun wondering if her poverty induced hunger was driving her crazy. The voice had eventually persuaded her she was not insane by informing of things she could never have known on her own, convincing Trixie the voice was not part of her damaged psyche.

In response to the cold and doubt, Trixie wrapped her torn cape around herself. The rough edges, worn down and dirty by the extended period of poverty she endured as a result of her show's failure following Ponyville, caused a surge of emotion to shoot through the showmare as it brushed her skin. The blue unicorn's hatred and loathing for Twilight Sparkle erupted like a volcano: It's all Twilight's fault that Trixie's career was ruined, that no one would pay one bit to see her perform, that she'd been forced to obey strange voices in her head! Who else could the blame rest with?

Firmly looked in this mindset, Trixie touched her horn to the runes etched in the floor, releasing a spark of magic into the complex. Just one little drop would be enough. Then the ritual would take over.

The chalk scripplings began to glow and steam began to rise from the elixers. Trixie, drawing on her occasional use of music in her stage shows, then used her magic to beat out a simple tune upon the drums. It began slowly, but picked up speed as the lights grew brighter, the steam became thicker, and an unearthly green glow enveloped the armor fragments.

TAP-TAP-TAP-TAP. TAP-TAP-TAP-TAP.

The glowing around the fragments intensified as they gradually began to meld together, slowly taking the form of a decript Grandfather clock. Once the clock was fully formed, a ghostly visage appeared, levitating in front of the numbers and hands.

The image was the translucent head of a stallion, wearing a raggedy, almost burnt hood. His face matched the cloak, for it was seemingly that of a charred, petrified corpse. The eye sockets, greatly expanded in the absence of most other facial features, housed two huge, yellow eyes, filled to the brim with hate and contempt. No eyelids could shield the world from this gaze, for the face was too burnt and crispy for them to move properly. In addition, his mouth seemed to be stuck in a crispy scowl. Had the phantom had functioning facial muscles, however, the wicked, arrogent laughter echoing throughout the castle halls indicated it would be wearing a triumphent grin.

At the apex of the ritual, the mane six and the Doctor burst into the room, the girls sporting the Elements of Harmony. The Doctor had brought them, claiming Princess Celestia instructed him to deliver them as part of his mission. In reality, he had used his TARDIS to avoid Celestia's barriers and "borrow" the Elements.

"Quickly! Use the Elements to disrupt the ritual!" The Doctor ordered frantically, fearing the return of his nemesis.

"Alright ladies, let's do it!" Twilight proclaimed, and each piece of magic jewelry began to glow as the six friends drew upon the magic of friendship. A rainbow beam was quickly summoned, and launched directly into the sickly green vortex surrounding the clock.

Instead of being destroyed by the blast, the clock began to glow, white light consuming it. The phantom's face also seemed to shift, but before the extent of the change could be seen, the whole thing exploded in a flash of light.

Not expecting this result, everypony was momentarily blinded by the light. Once vision had returned to all present, they beheld a horrific sight before them.

A pony (male, to be exact) stood before the grandfather clock. His coat was a darker shade of brown then The Doctor, and his mane was jet black. Interestlingly, his mane also extended onto his face, growing into thin strait mustache and beard. His cutie mark was a shattered pocket watch, glass cased cracked and gold chain shattered. A triumphent grin was spread across his face.

"Well Doctor, it seems that despite your best efforts, I have returned!" The new Time Pony exclaimed triumphantly. "Oh don't look so shocked, the whole universe knows I'm indestructible."

"D-D-Doctor? Who is that pony?" Fluttershy asked, intimidated by the Time Pony's intimidating resurrection.

"The Master."

*Cue Doctor Who end theme*

The Last of the Time Ponies

Chapter 3

The Master, having just cheated death yet again, wisely decided to use the first few moments of his new life to ignore every mare in the room and engage in witty banter with his arch-foe.

"Ah, Doctor, what a how good to see you again. I knew you'd show up uninvited to my little re-birthday party." The Master began, drawing out his words in the steady pace of a refined intellectual, in contrast with the Doctor's manic rambling.

Pinkie Pie was about to respond to the "re-birthday party" bit, but the Doctor raised a hoof to silence her as he began to talk, locking eyes with his arch-foe.

"Trapped inside the TARDIS after Luna turned the tables on you, you'd have ample time to work out a solution, but how did you get the showmare to help you?" The Doctor muttered, half asking the Master, half asking himself. "You psychic influence would have had to be magnified to overcome the Time Vortex's ionization bubble."

"An accurate hypothesis as always, Doctor. After I... miscalculated in my efforts to appropriate the Moon Princess's powers and created Nightmare Moon, my TARDIS was bonded to her, leaving me able to communicate only with Luna herself, and after a 1000 years of that foal, no one at all." The Master explained. "However, about three months ago, the forces that separated me from Luna and shattered my TARDIS along the fifth-demonsional support thread faded. I was able to bounce the psychic wave from piece to piece, using the shattered Time Vortex as a wormhole and amplifier. I then had the good fortune to form a link with this mare, her mind full of hatred and hunger for revenge."

It was then that Twilight put two and two together. "Discord escaped three months ago! His corrupting of the Elements let the Master escape!"

"And then you strung this washout along, pulling her strings, just another of your pawns." The Doctor stated with disdain.

"Nonsense Doctor. Trixie and I are partners in this venture, and after this day, she will be far from washed up." The Master replied while shooting his companion a smile. He also took the time to subtly grab his Tissue Compressor Eliminator.

While it was clear the Doctor wanted to continue this back and forth exchange, one pony's patience was at an end. "Alright bub, let's see how smooth you sound with a hoof in your face!" Rainbow Dash exclaimed. Her flank kicking instincts had been triggered, and in a flash Dash was charging towards the renegade Time Pony.

The Master instantly readied his Compressor, and sent a blast right at the rainbow blur. Luckily for the Element of Loyalty, the Doctor managed to grab Rainbow by the tail, pulling her to the ground and out of the laser's path. The Master and Trixie took the opportunity to flee into his clock, which had split apart to reveal an inside bigger then the outside.

The Doctor released Rainbow's tail just as the TARDIS's door closed, and the clock began to vanish, becoming transparent and hard to see. De-materialization was completed just as the Doctor leapt into the recently vacated space, his enemy slipping through his hooves by just a fraction of a second.

The Doctor stared ahead into empty air for a second, then hung his head, eyes closed, rueing his failure. He then turned to the Mane Six.

"So, I'm guessing I've got some explaining to do?"

The Mane Six nodded confirmatively.

"I thought I did."

The Master and Trixie now now stood inside a comfortably spacious white room in the shape of hexagon. The walls were studded with half sphere lights, and a control consel was in the center of the room. "Well, now that we are safely within the Time Vortex, I believe we should move ahead with the next stage of my plan."

"First things first, 'Master'. Trixie has upheld her end of our bargain, and now Trixie demands the power she was promised!" The azure unicorn spoke up.T

"Ah yes, of course Trixie, of course. You'll get what's coming to you." The Master spoke while opening a drawer on the control consel and removing an object similar to the Compressor, but with a glowing red light on the end.

After securing it in his mouth, the Master activated the device while pointing it at various spots on the floor. The Laser Screwdriver made a harsh buzzing noise. After a few seconds of this, a floor panel slid back, and a golden glow wafted out into the air. The Master stood back, an expectant look on his face.

"Well? Where is Trixie's power?"

The Master simply pointed down the hole. Slowly becoming skeptical, Trixie trotted over and looked in. What she saw took her breath away.

Beneath the floor panel were six orbs of golden light. The light they produced was a sickly, deathly kind of yellow, however, lacking a sort of glittering spark. The light began to enshroud Trixie as a feeling of power enraptured the unicorn. Her mane began to flutter on its own accord as pure power ripped through her veins. "Oh yes! Trixie can feel the magic!

After a minute or so of this, The Master quickly slid the floor panel back in place, blocking the energy flow. "That is quite enough of that, Miss Trixie. Any longer and you would have been reduced to ions and stardust." He stated in a rather unconcerned tone. "How do you feel?"

"Trixie is practically bursting with power! The Great and Powerful Trixie shall easily crush that insolent foal Twilight Sparkle and her meddling friends with this power!" The unicorn gushed.

"Actually Trixie, revenge may have to wait. As a matter of fact, I believe we should first focus on rebuilding your magic career." Spoke the Master as a malicious smile spread across his face, foreshadowing some wicked plan relating to the stage magician's career.

Back at Twilight's house, the bearers of the Elements have The Doctor strapped to a chair and wired to the machine previously used to test the Pinkie Sense, now converted into a polygraph.

Already suspicious of the so called 'Agent of the Princess', the Mane Six grew further suspicious when The Doctor's advice seemed to help The Master (which it had, as the Harmony blast had only repaired his decaying form), the way Doctor and Master knew each other so well, and how the Doctor could speak of such ancient events like they occurred yesterday.

When the Doctor attempted to put to rest their concerns with another flash of psychic paper, it backfired spectacularly when Applejack saw it for what it was: A blank piece of paper. Which lead us to the present situation.

"OK, mental note, psychic paper does not work on the bio-repositories for semi-sentient crystaline abstract intelligences." The Doctor muttered to himself while checking his restraints. "Still, I've been tied up in worse spots. Pleasent lot of captors at least." He then leaned in towards Rarity and Fluttershy, who were checking the wires. "Easy on the eyes."

Fluttershy turned bright pink and slinked away, horribly embarrassed, while Rarity appeared rather flattered. "Intelligent AND charming. Quite the combination." The unicorn's friends all gave her a look, causing Rarity to get ahold of herself, huff up, and walk away.

"Oh well. Not like charm can get me out of every predicament."

"Alright mister, stop giving us horseapples and tell us yer' story." Applejack began. "Even though the Princess said she was coming straight here to get the Elements, Canterlot is still a ways away, so why don't you pass the time wit a little story?"

"Well, I suppose I should start from the beginning." The Doctor began. "It all started a long time in the past, or is it in the future. I don't rightly know, what with the Wibbly-Wobbly Timey Whimey and all that...

A/N: OK, so I realized I should probably explain some of the Doctor Who parts to you non-Whovians.

First off, the Master is an evil Time Lord out to conquer the universe and the Doctor's arch-enemy, the Moriarty to his Sherlock. I'm going for the more collected, suave Master as done by Roger Delgado, for if I based him on the John Simm version we'd get a Discord re-run. Basically, if Discord is evil chaos, the Master is evil order, driven only to force all reality to bend to his will, a universe in perfect lockstep, every action dictated by him.

Psychic paper is blank paper that shows whatever you want it to show and never fails to convince readers (that's the psychic part). It isn't perfect though, and had been broken by a big enough lie (The Doctor wanted it to be an ID that acknowledged him as a "Mature and Responsible Adult.") Since a big enough lie could break it, I figured so could the opposite. Thus, upon closer examination, an already suspicious Element of Honesty Applejack saw through it.

The bit with the Elements is a reference to the classic serial The Deadly Assassin. In that, the Master is on his last regeneration, and it shows, as his body has become a rotted, shambling, burnt husk. He seeks to use the Eye of Harmony to repair his body and gain more regenerations. Since the Eye of Harmony could heal him, why couldn't the Elements? Which is why he had Trixie kill Derpy, in order to bring the Doctor who would bring the Elements.

Finally, Derpy's now dead husband being named Neighy was a joke based on recent Doctor Who companion Rory. Get it? Roar-y, Neigh-y? It's lame, I know.

Anyways, I hope that makes things clear, and I appreciate your feedback. Hope you've enjoyed so far!

Terror of the Autons

It is closing time at the Museum of Magical History in Canterlot. Celestia is guiding the sun in it's final descent down the horizon in preparation for her sister's raising of the moon. The sky is painted a brilliant dim orange.

A unicorn security guard tasked with closing the place up pauses briefly to observe the setting sun, then continues his rounds. A few minutes later, he changes course when a sound reaches his ears. The guard had never heard anything like it, but it sounded vaguely of piano wire grinding across metal.

The room the noise came from contains dioramas of civilizations predating Equestria. The unicorn casts as lighting spell as he walks amongst the wax dummies of the divided races. The security guard passes in front of the Pegasus exhibit. "Could'a sworn there were only four pillars in this one..." he mused upon counting the Roman (by our standards) columns.

After a few minutes of searching, the guard sighed in relief. "Must have been the pipes." He muttered while returning to his patrol, not noticing two new shadows lurking in the dark.

Just as lockup was finished, the sound of shattering glass filled the air. The security guard rushed to its source, a special exhibit on Industrialization-era City Life in Equestria. The culprit was a dark brown Earth Pony holding a glass sphere the size of a basketball. A blood red cloud seemed to swirl about within the orb. Most ponies became nauseous when viewing it, but the thief had a manic grin as he stared into its depths.

"You, stop!" Called the guard, but before he could take further action, he felt a jolt go down his spine as the world went black...

"Well done, Trixie. It would be wise to depart before further watchmen arrive." The Master stated to the azure unicorn, her horn still glowing from one of the magic spells the recently-empowered Trixie had learned in The Master's library of dark tomes and forbidden works. Trixie had been voraciously learning the dark arts, eager to find a spell that could destroy her rival. "We have what we came for."

A little bit later, back at Twilight's place, the ponies were growing a bit anxious awaiting the arrival of the Princess. The interrogation of The Doctor had long ago ended, and the Mane Six had quickly dismissed The Doctor as a rambling mad-stallion. I mean, flying all about space and time in a blue barn. What kind of preposterous non-sense is...

The narraration of the narrarater was suddenly interrupted by the rumbling of the pony in question's stomach. "Anyone got a jelly baby?" The Doctor asked.

Before anyone could respond, a flash of light filled the room. When the glare receded, everypony basked in the glory of the Alicorn Princess of the Sun. "Princess Celestia!" Exclaimed Twilight Sparkle.

"Yes, I arrived as soon as I could. I had total faith that you, my faithful student, could keep things under control until I could arri...." Suddenly, the Princess's eyes became narrow and her warm expression became an annoyed grimace. The cause of her sudden change in deminor? "Oh, it's you."

"Oh, Princess, how very good to see you again, you haven't aged a day!" The Doctor began to babble in a nervous voice. "Not your mane, though, that looks different. Did you do something with your mane?"

"Princess, are you acquainted with this pony? Have we imprisoned a friend of the Royal Family?" Gasped Rarity. "This is the... worst... possible... THING!"

"I was almost a member of the Royal Family, if you can believe that one." The Doctor responded while staring off into space. "Funny story about that..."

"Doctor, just what are you doing in Equestria?" Princess Celestia interjected quickly. "I believe I asked you not to return to my kingdom after the incident with the Sea Ponies."

"They were trying to drown the entire planet!" The Doctor yelled in an exasperated tone.

"You teleported them into my sun!" The Princess yelled back. "Which, I might add, I'm still trying to get all the spots out of!" The Princess suddenly realized how she was appearing to her subjects. Twilight and Rarity appeared shocked that a mere mortal could get such a rise out of a goddess, Rainbow Dash was looking back and forth between The Doctor and Celestia, watching the argument like a tennis match, Fluttershy was backing into a corner, frightened by the shouting, and Pinkie was munching on a cupcake with a giant foam finger that declared Celestia to be number one.

The Princess took a moment to compose herself. "Why have you sought the Elements, Doctor?" She asked while magically removing his bonds.

"The Master is back. He has a unicorn in his thrall and a functional TARDIS, and has already killed one pony." The Doctor replied, suddenly grim and serious.

"The same Master that we battled for the Elements of Harmony?" Celestia asked.

"You helped the Royal Sisters find the Elements?" Asked Twilight. Realization dawned on her face. "I've read about you! You're the Sainted Physician! The one who lead the Sisters through the chaos of Discord's reign to the Elements!"

"The Sainted Physician? Is that what you call me now?" The Doctor asked incredulously. "I mean, it has a nice ring to it, sure, but I introduce myself as The Doctor for a reason." He then looked over to Twilight. "And yes, that was me. The Master was in rather poor health at the time- he claims I forced him to go through his regenerations too fast, I say too many fatty hay fries- and wanted to use the Elements to heal himself. He failed, but now he seems to have tricked us into doing it for him."

"And that is precisely why YOU must stop him Doctor." Celestia spoke up. "Twilight and the Element bearers will assist you in this." The Sun Princess decread before leaning towards her prize student. "Contact me if he gets out of hand." Returning to normal, she asked "Is there anything you require of the Royal Guard?"

"No, The Master is brilliant at personal disguise, has a fully functional TARDIS, and is capable of completely hypnotizing anypony with a weak mind (and from I've seen, there's a lot of them around these days). If we move openly against him, he'll simply flee and try again. We need to wait for The Master to make the first move, then ensnare him." The Doctor explained. "Now, is their anything else I need to know? No, brilliant." He then turned to Twilight. "With your permission, I'd like to work out of this library. Lots of information, in case The Master breaks out some ancient super evil. Oh, and don't worry, the only space I need is room for a phone barn." The Doctor blinked. "Which I should probably go get." He added before galloping off, leaving an awkward silence in the air.

"He's funny." PinSkie commented in a subdued tone. She then burst out "I LIKE HIM!"

"So Princess Celestia, what exactly is your relationship with our dear Doctor anyway? I don't think it was made very clear." Rarity asked with just a hint of sarcasm in her voice.

"I wish you best in this battle, Twilight. You're going to need it." Princess Celestia spoke up (completely ignoring Rarity) before teleporting away, back to Canterlot

"I must say, Mister Saddleton, this ah, this order," spoke an Earth Pony sitting at a desk. His well groomed red mane stood in bright contrast to his light green coat. His cutie mark was a package of plastic wrap. "We appreciate your business of course, but it's just a tad bit unusual for such a prominent customer to pop out of the blue."

"Well Junior Smith, the person I represent can never have enough plastic." The Master, masquerading as a business pony named Harold Saddleton, replied. "Now, if it isn't much of a bother, might I inspect the plastic forges? Seeing as I have hired out all of them..."

"I'm afraid I can't do that, Mister Saddleton. Company policy, you understand." Junior Smith replied. In response, The Master locked eyes with the business pony, causing Smith to become unnerved.

"Come now Junior. We're friends, are we not?" He spoke re-assuringly. All of Smith's apprehensions seemed to melt away as The Master used his hypnotic powers.

"Most certainly Mister Saddleton!" Junior Smith stated. "I suppose a little tour won't do any harm?"

The very next day, The Doctor is at his desk, leafing through several newspapers, looking for any crimes carrying The Master's trademarks. A loud belch broke his concentration, and a few seconds later Spike walked in with parchment from the Princess.

"News from the Princess, Spike?" The Doctor asked.

Spike nodded. "Seems someone stole something from the Museum of Magical History last night." He explained while handing the papers to The Doctor. "So, Doctor, what exactly were you talking about being a part of the Royal Family last night? Are you and the Princess... well, you know..." Spike asked somewhat awkwardly. Then he perked up and added on. "And if you did bang the Princess, can you give me some advice on mares?"

The Doctor became flushed and awkward at the dragon's question. "Well, um, you see, I'm not sure you should be asking me specifically..."

"Doctor, did I hear we have word from the Princess?" Twilight called out, and the boys could hear her moving along the stairs.

"We must certainly have, Twilight." The Doctor replied. "It seems that yesterday, the Museum of Magical History was broken into, and the..." He checked the paper again, as his eyes widened in disbelief. "Soul Sphere of Duke Sun Beam! What was that infernal contraption doing on display?" The Doctor flipped through the pages. "Limited exhibition signed off by... Prince Blueblood? Maybe I shouldn't have left the God-Queen at the alter, the Royal gene pool might have been graced with some brains..."

"I've read of Duke Sun Beam. He attempted to assassinate the Princess during the Industrialization-era. But I've never heard of this Soul Sphere." Twilight Spoke up.

"It's a magical item, not the kind they teach you in school however." The Doctor began to explain. "You see, Sun Beam was a member of a secret order known as Faction Eclipse, a collection of families that posses great wealth, but for whatever reason, little in the way of social prestige. Their purpose was to free Nightmare Moon and aid her in deposing of Celestia and her nobles, whose places they would take. Children born into the order are given a public, sun related name, while a secret name, signifying their real loyalty, would be used amongst other Faction members. They also developed spells that could create illusionary cutie marks. Handy, since their true cutie marks often represented ghastly talents such as robbery, murder, arson, the like."

"What was Sun Beam's real name?" Asked Twilight.

"Moon Thorn." Answered The Doctor. "He was an industrialist with a factory in Trottingham, the very first manufacturer of plastic in Equestria. The sphere, you see, stored souls. At night, he and his Faction Eclipse droogs would drop the illusions, don cloaks and masks, and stole the soul from anypony that crossed their path. The souls in the Sphere could then be used as fuel to animate plastic objects. The stolen souls were burnt like coal to power mannequins that he used as free labor and expendable soldiers. Midnight Autons, the petrified city dwellers called them. His eventual goal, however, was to used the combined power of every soul in the city to transfer Nightmare Moon's soul from the moon to a plastic body of his own creation. A poppycock plot doomed to fail before it began, but in his madness Sun Beam killed over 40 ponies, most of them homeless vagrants."

Twilight was aghast at such a gruesome use for magic. "That's... That's horrible!" She gasped, too shocked to be articulate.

"Indeed. And now such a infernal device is in the hands of that mad pony The Master."

About a week later, the subject of the last lines is examining the plastic forges at Junior's plant. The factory owner himself follows The Master absentmindedly, with a blank look on his face. "Excuse me, Smith, but may I enquire as to where our finished product is?" He asked, snapping the brainwashing victim from his stupor.

"Right this way Harold." He stated, and quickly lead The Master to a large container loaded with the finished product. "I must say Mister Saddleton, those new methods you introduced have had amazing results. The legs are particularly impressive. If this doll had a brain in it, I'd go as far as to say it could get up and walk away!"

"Now isn't that an idea?" The Master asked rhetorically while examining one of the hundreds of Great and Powerful Trixie dolls. "You done a commendable job on my employer's likeness. We are pleased by your results."

"Thank you Mister Saddleton."

"TWILIGHT! WE FOUND THAT NO GOOD VARMIT!" Came the heavily accented voice of Applejack as she and Rainbow Dash burst into the library. The Doctor, Twilight and Spike rushed to the main room to meet them. "We know where Trixie is!"

"OK,so I was flying up in the sky, practicing being awesome, when a jet stream smacked me in the face with this!" Rainbow Dash explained, holding up a piece of paper. Closer inspection revealed it to be a flyer for Trixie's magic show, now operating in and around Staliongrad. The advertisement was dominated by Trixie pulling a rabbit out of a top hat. A top hat held by The Master, who seemed to be staring right out of the paper, gazing into the soul of the onlooker.

"What's your game?" The Doctor mumbled as he dug through his desk. He eventually returned with his all-purpose sonic screwdriver. A humming filled the air as he ran the device across the poster. "Ah-HA!" He exclaimed as the Trixie portions of the picture began changing colors. "He using psychic paper, alien pheromones and images of him and Trixie to hypnotize passing ponies to see the shows!"

"Den how come we ain't hypnotized?" Applejack asked.

"Well, this is built to work on ponies, so Spike here is protected because he's not a pony." The Doctor explained while pointing to the dragon. "Your Elements of Harmony protect you ladies. As for me... Let's just say The Master's tricks haven't worked on me for a long time."

"The Master is hypnotizing ponies to go see Trixie's show, but what for?" Twilight pondered. "Does he intend to steal their souls for a plastic army?"

"Dosen't matter!" Rainbow Dash declared. "We know where he is, let's go mash 'em up!"

"Easy there sugarcube, don't get yourself worked up." Applejack advised. "Staliongrad's a long ways away, so we'll need to pace ourselves if we wanna be in fighting shape when we arrive."

"Oh you ponies, and your long distance travel plans." The Doctor said with a chuckle. "I think I've got a shortcut." He added while gesturing to the blue barn in the library corner.

*Cue Doctor Who theme*

A/N: More notes for those unfamiliar with Doctor Who.

TARDIS: Time And Relative Dimensions In Space. An invention of the Time Lords, a TARDIS is like a massive time traveling motor home. It is far, far bigger on the inside then the outside, with The Doctor having offhandedly mentioned a pool and a library in the past. TARDIS can travel through time and fly through space like a space ship, but most often go from place to place via dematerialization and rematerialization.

A key component of any TARDIS is the Chameleon Circuit, which disguises the TARDIS as something appropriate for the time and place. However, to save money during the show's early years, the Chameleon Circuit in The Doctor's TARDIS was broken in the first episode, leaving it stuck in the shape of a police box (ponytized to a polic barn). This has since become iconic to the series, and as such, has not been changed, despite more then enough money in the props budget to do so. The Master's TARDIS, however, is fully functional, and as such, can shapeshift into any form.

All that business with Princess Celestial is a reference to the running gag that The Doctor... Invalidated the title of The Virgin Queen Elizabeth the First.

The latest incarnation of The Master used the alias Harold Saxon to run for Prime Minister. So I ponyized it to Harold Saddleton.

Next time on Doctor Whooves: The Mane Six and The Doctor must wade through shadows and lies to stop a mass murder in THE CARNIVAL OF MONSTERS!

Carnival of Monsters

The unmistakeable sound of a TARDIS de-materializing echoed throughout the dry air. The blue box blinked into existence in the shadow of a large circus tent. The Doctor was the first to exact. "Right, here we are. So what did you girls think of your first TARDIS flight?" He asked.

"The magic needed to make such a thing possible... Doctor, your machine is fascinating!" Twilight gushed as she exited the machine.

"I don't know." Spoke Rainbow Dash as she stepped out. "It's fast in the sense that we got here in ten seconds flat, but it's not... You know..." Dash thought about what word to use. "Vroom Vroom fast, you know what I mean. Plus, it seems like the interior was built out of scrap!"

"I concur Dash." Rarity added. "The machine is marvelous, but needs a serious re-decoration! I mean, sink faucet dials and typewriter keyboard? Steampunk went out of style some time ago!"

"To be honest, the whole trip was kinda scary. I mean, it sounded so creaky, I thought we were going to fall apart!" Fluttershy squeaked out. "But I'm sure you keep it in very fine condition Doctor!" She added upon realizing she may have insulted The Doctor's mechanical skills.

The Doctor frowned. "What's wrong with the noise? I happen to like the noise, it's a brilliant noise."

"Noise or nawh, it got us here in one piece, and mighty quick too." Applejack drawled while joining her friends. "That makes it ok in my book." Pinkie hopped out right after, munching on a cupcake.

"Pinkie, where'd you get that cupcake?" The Doctor asked.

"Cupcake button." She stated simply.

"Didn't realize I had one of those." The Doctor replied simply. He then took notice of a sign. "Ringleader Circus, now featuring the Great and Powerful Trixie. We're masters of entertainment." Spoke the Doctor. "He never was big on subtlety..."

"Say Doctor, this has been bugging me for awhile now," Applejack spoke up. "If your TARDIS travels through space AND time, why don't we just go back before this started and hog-tie Trixie before she even frees The Master?"

"That would be crossing our own timeline, Applejack. If we went back in time and did that, the course of time would be altered, and this moment, in which that descion was made, would no longer have occurred, giving us no reason to go back, creating a paradox." The Doctor explained. Twilight, Pinkie Pie, Fluttershy and Rarity seemed to get it, but Rainbow Dash and Applejack were still struggling with the concept. "Look, just mull it over while I step back into the TARDIS. Seeing as we are at a circus, I feel I should disguise myself with a little more color."

Rarity spoke next. "You know Doctor, you've made me curious now. What kind of fashion do they have on your planet?"

"I never was one to keep up with that sort of thing, but robes, collars, caps, stuff like that." The Doctor called from within the box. "I think you'd like it, honestly." Then, he stepped out, inflicting nightmares on the fashion pony for years to come.

"If it even remotely resembles that technicolor monstrosity you are currently wearing, I doubt I can appreciate your people's fashion even slightly!" Rarity exclaimed. "I mean, the stitching, the colors, where would I begin to make you presentable!"

The coat The Doctor had slung on was indeed hideous. A selection of colors seemingly selected to clash were stitched together in blizzare shapes, no sense of pattern, unlike the neatly ordered lines on Rainbow Dash's mane. "First of all, this is the height of fashion on 67th century Kracnkonelia, and second, we are at a circus and I want to blend in. So shall we persiste in babbling or shall we pursue our goal?"

Little did they know The Master was already watching them. After forming an alliance with the mare running the once failing circus, he had rigged the area with all manner of sensors and scanners, so he'd know exactly when his nemesis arrived.

The Master smirked. He was safe inside his TARDIS, while The Doctor and company were stumbling about in the dark. Time to spring the trap. Activating a radio, The Master gave the word. "Silver Standerd, those guests I informed you of have arrived. Please take the steps we discussed." He then changed the communicator's channel. "Trixie, our act has begun. Remember now, Twilight is in the audience." He then took the time to indulge in a little evil laughter.

Back outside, the Mane Six and Doctor had split up to cover more ground. Applejack and Rainbow Dash, Fluttershy and Pinkie Pie, and Rarity and The Doctor were the groups, while Twilight had gone searching for Trixie, wanting as few ponies as possible in the middle of a likely wizard battle, as The Doctor correctly guessed The Master had increased the showmare's power.

Let's focus on Fluttershy and Pinkie Pie to begin. The two trotted about the fair grounds, keeping eyes open for anything odd. A twitch of the Pinkie Sense caused the party pony to cast a suspicious gaze towards a clown pony pushing a ballon cart. She motioned to Fluttershy, who locked eyes with the Clown. The two stared each other down amidst the crowd, which remained oblivious to the struggle. Finally, after ten minutes of continued staring, Fluttershy was finally forced to blink by the inpony hareliquien.

"Pinkie, we need to hide." Fluttershy stated as the Clown began moving towards them.

"Yay, hide and seek!" Pinkie exclaimed, until Fluttershy shot her a withering glare The party pony nodded and the two rushed off. Despite their efforts, the Clown kept up, refusing to be shaken off. "Quick, in here!" Cried Pinkie upon sighting a House of Mirrors. The two mares ducked inside, causing the Clown to finally come to a stop, gazing soullessly at the building.

"Hey Applejack, look at this." Rainbow Dash said on the other side of the circus. "Seems they have a Pegasus performing here-'Zig Zag, the fearless psycho of the sky.' I say we check this out! This pony could be connected to The Master!"

"Uh huh. I'm sure this ain't at all motivated by the "Greatest Flier in Equestrian" tag line they put on there." Applejack responded, causing Rainbow to become indignant. "Still, I reckon we should check. The pony on that there poster don't look right in the head. She could be connected to The Master."

The two entered the tent, and Rainbow Dash instantly became suspicious. This tent wasn't nearly big enough to do stunts in, and that's ignoring the fact that the open sky would have been preferable to any size tent. The mystery deepened when a sheet covered orb taller then ten ponies was rolled in.

"Mares and gentle-stallions, welcome to our show! Today, our very own Zig-Zag will be flying at breakneck speeds..." The sheet was pulled back, revealing the object to be a giant glass orb on a stand, like a big snow globe. Only instead of a winter wonderland, the sphere held only a very mad pony. "...within this glass orb!"

The crowd let out a gasp, wondering how a Pegasus could maneuver is such cramped space. "Are you ready Zig-Zag?" Asked the announcer.

Inside the bubble, the mad pony nodded yes. The Pegasus had a manic grin that could give Pinkie Pie a run for her money. Her body was crisscrossed by streaks of bright electricals colors, but with no symmetry of any sort. A jaddged lightning bolt cutie mark that bent at several angles rounded out the appearance of a pony that practically oozed madness.

In a flash, Zig-Zag charged towards the glass, only to pull an impossibly shap turn, changing course towards the roof of the sphere, only to shift course again. The flyer continued to rocket around the tiny space, her tail resembling a multi-colored lightning bolt. Even Rainbow Dash was impressed by this display. While Zig-Zag's top speed was in fact a great bit slower then the Element of Loyalty's, the ability to pull of such tight turns was immensely impressive.

For one split second, the eyes of the two flyers connected. Eyes growing wide, Rainbow grabbed Applejack and yelled one word.

"DOWN!"

A split second later, the glass exploded as Zig-Zag shattered the barrier a rocketed at the two Element bearers. Had Rainbow not ducked, the two would have had their heads taken off.

Unfazed by the miss, Zig-Zag made a hard left and came around again. Dash was already in the air, charging hooves first into the spot Zig-Zag would fly through in a moment. The crazy pony stunned everyone, however, by rapidly changing course, leaving Dash with nothing but air. A split second later, the electric trail wrapped around Dash as Zig-Zag literally flew circules around the Element bearer, pummeling her with punches and kicks, rushing to punch her exactly 180 degrees away from the previous blow, keeping Dash locked in vortex, which was also having its oxygen funneled away.

Thinking quickly, Applejack looked for something to help her friend. She found some construction rope behind the bleachers, and quickly fashioned a lasso. "Gotta time this right..." She muttered while taking aim. The rope flew true, and ensnared itself around Zig-Zag's leg. As she was pulled to the ground, the madmare sunk her teeth into Dash's side, dragging her to the ground as well.

Rainbow had taken a beating, and though she was still breathing, it took her a minute to climb to her feet. Zig-Zag however, was back on her feet in an instant, ready to brawl with Applejack. Before the fight could begin though, the announcer ran up to Zig-Zag. Everypony else had fled.

"Zig-Zag, stop this right now!" He demanded. "Look, let's get you back to your tent, you need to take your meds..."

Before he could continue though, Zig-Zag tugged on the rope, yanking it from Applejack's grasps. She then snapped it like a whip around the announcer's neck. Then with a tug, she jerked the coiled rope back and snapped the announcer's neck. Not caring that her senseless killing had weighed her down too much to fly, Zig-Zag turned to Applejack. "Now, did you want something?" She asked in a chillingly childish way.

Applejack adjusted her Stetson. "Girl, I'm tan your hide 'till you're just one color: Raw red."

While the rather brutal fight that ensued was being built up (the four groups adventures are all happening simultaneously) Rarity and The Doctor were examining the area around the sleeping tents. "Excuse me folks, are you lost?" A perky voice asked. And crud, they're caught. "Judging by your coat, you're here to apply for a clown position. I'm sorry, but none are currently available."

"Oh, I suppose we are. That's what's neat about being lost: You never know you're lost until someone points it out. We'll be on our way." The Doctor stated in a hurried tone. "Come along Rarity, let's not waste anymore of..."

"Silver Standerd." Introduced an Earth Pony mare. The name was fitting, for both her mane and body were a gleaming silver. Silver Standerd's cutie mark was a trio of bits. "And it's no problem. Enjoy the circus. Oh, and ma'am!" She called to Rarity as the two left. "We sell these flowers as a souvenir, they only grow in this valley. Take this as a personal gift." Silver added while passing an exquisite subdued blue flower to Rarity, who immediately affixed it to her hair.

"Oh, thank you. It certainly is lovely." She commented while galloping off to rejoin The Doctor. As soon as they left Silver Standerd's smile faded, replaced with a cruel scowl. She pressed a hoof to an ear, activating her headphones. "Master? Everything went as you predicted."

Once Rarity caught up The Doctor, she tried to draw his attention to her mane dwelling flower, but the Time Pony was staring slack jawed at a vending machine propped against a tent. "The Snack Master." He read quietly. "Only he would be so bold." The Doctor walked towards the obviously disguised TARDIS, the thing opened, splitting down the half, just at the right moment to smash into The Doctor's head.

"DOCTOR!" Rarity exclaimed, but her further cries where silenced when the extraordinarily well crafted plastic flower notched behind her ear sprang to life and constricted her neck, strangling her to sleep.

Inside the TARDIS, Trixie had joined The Master in the screen room ,observing the ponies being snared in traps and tricks. This last one unimpressed her. "Really? You hit him with a door?" Trixie asked with a raised eyebrow.

"Sometimes a trap's brilliance is its simplicity." The Master explained. "Now, you have a show to perform. Silver Standerd!" He called into the communicator.

"Yes Master?"

"Two more to dispose of."

*Insert Doctor Who theme here*

A/N: More notes!

First, if anyone is a bit perplexed by the sudden friendliness The Doctor and Mane Six have developed, it's because between The Master stealing the soul sphere and the discovery of the flyer, he'd been living in the library. Well, he'd been living in the TARDIS, which he parked on the library's rug. They all became friends during that time.

The coat the Doctor is wearing is the one used by his Sixth incarnation. A mind meltingly ugly costume, the actor playing the Doctor (Colin Baker) hated it and wanted the Doctor to wear a leather trench coat, since this was a darker Doctor, but was rejected. And thus, a terrible costume was born. I'm not sure how you put pictures in these, but if someone leaves an image in the comments section, you'll see what I mean. Rarity would be sickened.

Next time, on Doctor Whoof! With the Doctor and his friends trapped in a circus of nightmares and blood, can he and the Elements of Harmony escape without being shredded by THE TALONS OF THE GREAT AND POWERFUL TRIXIE

The Talons of The Great and Powerful Trixie

Inside the House of Mirriors, Pinkie Pie and Fluttershy trot about aimlessly. After fleeing inside to escape the robotic clown, the two ponies could not find a way back out. Unbeknownst to them, the front and only door had been blocked by a sliding mirror. The entire building was a massive trap.

"You'll stay close to me, right Pinkie?" Asked Fluttershy, frightened out of her mind by the warped reflections of her and her pink friend. When she glanced over to her right, however, all she saw was another reflection. "Eeekk!" She squeaked out, then began to back up. "Pinkie Pie? Pinkie Pie? Please don't leave me alone in here... I... I can't..." Upon realizing her friend was gone, Fluttershy backed into a corner and sobbed tears of loneliness and fright, warped reflections her only companions.

"Fluttershy! Fluttershy! This is a really bad time to play hide and seek!" Pinkie called out after realizing her friend had vanished in the blink of an eye. The party pony continued to trot about, calling her friend's name, only getting a response after several minutes.

"What, has Fluttershy ran off partner?" Came the unmistakable drawl of Applejack. Pinkie excitedly looked to her friend. The farm pony was within one of the mirrors, taking the place of the Element of Laughter's reflection.

"Applejack, I'm so glad to see you! Help me look for Fluttershy, she's gone missing and I can't find her and..." Pinkie babbled as she walked, Applejack trotting along with her.

"Slow that stampeding mouth there, sugarcube." Applejack interrupted. "Your non-stop babbling is probably what drove timid little Fluttershy away! That constant jowling of yours is mighty annoying, and that's the truth!"

Pinkie was taken back by the reflections harsh words. Her mane seemed to quiver a bit, but remained puffy.

"Yeah! Your pranks are no fun, and you're totally fat and flabby from all those sweets! Totally lame!" Spoke a new reflection from across the hall. Pinkie turned to see Rainbow Dash in another mirror, sticking her nose up at Pinkie.

"And those utterly tasteless parties you throw!" An illusion of Rarity chipped in. "Tacky decorations, bad food, atrocious party games... Need I go on?"

Finally, an illusion of Twilight Sparkle appeared. "You're a loud, obnoxious, annoying pest Pinkie Pie! I've hated you from the moment I saw you! You couldn't just leave us all alone!"

"Your parties are lame!"

"Your mane is hideous!"

"You're a total moron!"

"WE ALL HATE YOU!"

This all proved to be too much for Pinkie Pie, whose mane fizzled into a straight style as she collapsed into tears. As she lay bawling on the ground, one of the mirror walls behind her receded, opening a path to a very familiar scene.

"Pinkie dear, won't you join us for a while? There's somepony we need to talk to you about, the delightful Mister Master...." Called the voice of a sophisticated French woman, inviting the despairing pony to a very mad tea party...

Back inside The Master's TARDIS, the evil Time Pony sits at a console, wirelessly operating the sliding walls, audio projectors, and hologram screens inside the House of Mirrors. "Do you see now, Doctor, just how hopeless your cause is? All but one of your allies, I have vanquished, without even needing to leave my own TARDIS!"

The object of his gloating was, of course, The Doctor, who sat tied to a chair in the same room. "You managed to get a young mare with the mind of a four year old to cry. Truely the machination of an unstoppable diabolical mastermind." The Doctor remarked in a casual way. Despite his indifferent response, the Time Pony was very concerned for Pinkie, but could not allow The Master to know how effected his was.

"Does another dead companion mean so little to you Doctor? Perhaps the uncounted years of watching your mortal friends wither and die has finally made you indifferent to the lives of lesser beings." The Master responded. "There may be hope for you yet."

"Another factor to distinguish ourselves from one another, eh?" The Doctor rebuked.

"You sell yourself short, Doctor. You are very much similar to me, as am I to you." The Master retorted. "We have both rejected the worthless traditions of our people, choosing to employ our vast Time Pony powers to alter the universe and its history."

"Your changes to the universe have produced nothing but death and strife." The Doctor insisted. "I have always attempted to save life."

"For a man who calls himself The Doctor, you have engaged in acts of bloodshed that even I find impressive." The Master insisted back. "The Sea Ponies, the Dalek breeding ship, Mondus, the last Queen of the Parasprites..."

"The actions of all of those put countless innocent lives at stake! I had to take whatever I action I could to save the victims!" The Doctor exclaimed.

"And now you shall sit helpless, as I launch a devastating attack upon the Equestrian people, one that will only end when the Royal Sisters banish themselves to the Moon for eternity, and grant me the throne!" The Master proclaimed. "In approximately one hour, I shall activate the Soul Sphere, and the plastic Trixie action figures and other merchandise I manufactured under its magic and sold here will spring to life, killing everypony they encounter."

"Your insane, Master. The Princesses will not be cowed by one measly terrorist attack." The Doctor responded.

"In that, you are correct, Doctor." The Master conceded. "Which is why it is only stage one of my plan. The Sphere can absorb the soul of anypony killed by an Auton it created, giving me enough power to bounce the signal off the moon, casting the spell over all of Equestria, turning every inch of plastic into an Auton servant of The Master!" The mad villain become intoxicated at the thought. "Toys strangling fillies in their cribs, chairs swallowing weary ponies whole, shop mannequins turning stores into bloodbaths!"

The Master stopped abruptly, taking a breath to calm himself down. "The Royal Sisters will have to travel to the Moon together to block the spell. And well, let's just say I've left them a little surprise..." He smirked at an aghast Doctor before facing one of the monitors. "Oh look, it seems Trixie's show is about to begin. Miss Sparkle seems to have found herself a good spot. What do you say Doctor? One last magic show before dying?"

As the final preparations for Trixie's show were being completed, two henchmen were inside the House of Mirrors to collect Fluttershy. They so startled the inconsolable Pegasus that she flew straight up into the ceiling and knocked herself out on the ceiling.

"Well, that was easier then I expected." Quiped one goon.

"Alright, let's get this over with." The other replied. "The Manticores need to be feed, after all."

Inside the largest circus tent, the main event was about to commence. Ponies had found themselves drawn to the spectacle from far and wide, not completely comprehending the attraction but arriving never the less.

With a flash of smoke and lights, Trixie took the stage. "Ponies of all walks of life, welcome! Prepare yourself for the greatest display of magic you shall ever see! Bask in the magnificence of The Great and Powerful TRIXIE!"

And so the act began. As Twilight watched the typical magic tricks (flowers out of hat, disappearing, card tricks, etc.) she couldn't help but feel Trixie had more up her sleeve. When she was performing in Ponyville, she was pushing herself to the limit to complete her act, but now, these tricks seemed to be afterthoughts. "Perhaps The Master has increased her power, as The Doctor suggested." Twilight mused, despite all her years of study suggesting such a thing to be impossible.

"And now, for Trixie's final trick!" The showmare declared. "The Great and Powerful Trixie will run seven swords through this box..." she explained as lights illuminated a large green box suspended overhead by cables. "...Without harming my assistant, the Drab and Unfabulous Rarity!"

The crowd gasped as the box swung open, revealing a bound and gaged Rarity inside. No one could tell she was restrained, however, as the cloth used to tighter hooves and mouth was the same color as her coat. The box swung shut, and Trixie moved seven swords around the box, three on each side and one above.

At the sound of this, Twilight took to the stage, putting little faith in the magician's declaration. "Trixie, stop this madness, stop it right now!"

"Well, look what the cat dragged in. Have you arrived to try and humiliate Trixie again?" The magician ranted. "You shall not best me a second time Twilight! I shall vanquish you and end our rivalry once and for all!"

"Humiliated you? Trixie, I was keeping everypony in town from dying!" Twilight retorted. "Please listen to me! The Master has taken over your mind. You're cocky and arrogant, but you're not evil! If you stop now I'll speak on your behalf to the Princess to clear of what The Master made you do!" Twilight offered, remembering the Smarty Pants incident as an example of how magic can mess with a pony's mind. "Let me help you! We can be friends!"

For a moment, Trixie's resolve seemed to falter. But then, her expression darkened as the glow of magic encompassed her body. "No, Trixie will not be deceived by you! The Master has given me something greater then friendship!" She declared while building up a spell. "POWER!"

Electricity cracked across the air as the crowd scattered, conveniently mixing in with the crowd fleeing Zig-Zag's "show." Twilight used her own magic to transmutate the bolts of lightning into coils of rope, which she launched at Trixie in an attempt to restrain her. Trixie responded by bringing the swords close and chopping the ropes to bits. The deadly blades were then launched at Twilight.

With a flash of magic, Twilight turned the serrated swords into a rubber chicken, a beach ball, a bucket, a sword shaped puddle, a newt, a puff of nitrogen gas and a bunch of super balls. "I can take whatever you toss, Trixie." Twilight stated simply.

"Trixie will make you eat your words, bookworm!" Trixie retorted while teleporting in several large dictionaries, then hurled them at Twilight. The lavender unicorn managed to dodge the tomes save one, which impaled itself on her horn. With a look of determination, Twilight set the book ablaze, then threw the fire around Trixie, trapping the showmare in a ring of flames.

"Trixie, I'm offering to help you one more time. Stop this fight." Twilight stated, now with a look of finality on her face. Trixie seemed desperate. She looked at the fire, then at Twilight, then the fire, then Twilight, fire, Twilight. Finally, with a smug look on her face, Trixie closed her eyes and cast a spell.

The ring of flames exploded in a scorching fireball. Twilight cast a powerful barrier spell to keep the fire contained. The purple magic dome bulged as the fire tried to escape. Twilight was forced to avert her eyes, but eventually the fire burned out, and the shield, and an exhausted purple unicorn collapsed to the floor.

After a few moments, Twilight cracked an eye open, only to see a hole in the stage where Trixie, then the inferno, had raged. "T...Trixie?"

Next to Twilight, the floor exploded. Trixie levitated herself through the opening, her usual magic aura replaced by cold darkness. "Now Trixie shall end you, Twilight Sparkle!" she declared while levitating another sword from off stage.

"Another... Sword?" The weary Twilight asked.

"Trixie always has spare props." The azure unicorn declared smugly while lifting the blade overhead, taking a step forward, preparing to cleave Twilight in two.

Twilight had come up with a last minute plan, however. Using her last drop of magic, she rolled the super balls a sword had been transformed into Trixie's path. The azure unicorn unwittingly stepped upon them, rapidly losing her balance and falling on her rump. The sword's magic aura evaporated, and buried itself in the wooden stage an inch from Trixie's head. The shock of almost bring killed, plus the sudden retreat of her dark power, and the fatigue of magic use catching up, finally caused Trixie to pass out.

"That's... Disappointing." The Master remarked with a scowl as he watched Twilight tie up her defeated opponent. "Still, she handled the power rather well, and pulled off a decent manuver..." he continued while focusing on his control panel, hitting switches and pulling levers.

"Hate to interrupt, but in order to transmit the activation signal to all your Autons, you'll need a Trans-Wave atmospheric wave amplifier, correct?" The voice of The Doctor asked.

"Why of course, Doctor. But you'll never be able to disable it from your location, seeing as it is installed..." The Doctor then let out a deep sigh. "You're out of the chair, aren't you?"

"Yep!" The Doctor replied, standing over the just mentioned component. "I could've gotten untied whenever, but I waited until you were distracted enough to grab this." He added before crushing the crucial component underhoof.

"It seems you have defeated me this time Doctor, but I shall return!" The Master declared. "TARDIS, emergency code D-42!" The familiar whirring noise filled the air as the Master's TARDIS de-materialized around The Doctor, taking his arch-foe with it.

"And I'll be waiting for you."

Without The Master calling the shots, the rest of the villains were quickly arrested. A Royal Guard paddy wagon, apperantly deployed by Celestia after a worried Spike sent her a letter, arrived shortly after. The royal guards rounded up the criminals with robotic efficiency while Twilight tended to her friends.

Rarity was levitated down from her precarious perch, Rainbow Dash and Applejack given first aid after Royal Guards finished subduing a battered Zig-Zag, Fluttershy was given a towel to clean off the Manticore drool after she was pulled out the animal cage and away from the mistreated and in need of kindness animals. As for Pinkie Pie...

"Pinkie, The Master has escaped, but we have his goons in custody. We need to leave." The Doctor spoke, having entered the House of Mirror's back door with Twilight.

"Oh no, I'm not going with you meanie-pants wearing meanies!" The straight maned pony declared. "I'm with my REAL friends now!"

"I am not in the mood to deal with this." The Doctor stated wearily. "Don't worry Twilight, I've got this." He added while approaching Pinkie.

"I'm not going anywhere with you, Doctor Jerk!" Pinkie shrieked. The Doctor knocked over the pile of rocks as he walked. "YOU KILLED ROCKY!"

The Doctor simply rolled his eyes and headbutted Pinkie. With an audiable crack, the Party Pony feel to the floor.

"PINKIE PIE!" Twilight exclaimed, shocked at the sudden turn of events.

"Don't worry Twilight, that was a psychic headbutt." The Doctor explained while rubbing his sore head. "I've transferred the truth about The Master's trick into her mind, she'll be fine."

With apprehension, Twilight asked softly "Pinkie Pie, are you okay?"

"PARTY TIME!"

"She's fine."

"TWILIGHT, COME QUICK!" Called Rarity, and the three galloped out to see what was amiss.

The sight that greeted them required no words. Two Royal Guards were scattered in pieces across the ground, the bloodless dismemberment indicating they were plastic Autons. Ahead of them, the paddy wagon, surrounded by unshackled hoof-cuffs, was fading out of existence, the sound of The Master's triumphant laughter echoing across the empty circus.

Inside the fleeing TARDIS, The Master addresses Zig-Zag and Silver Standerd. "You have both proven yourselves to be exceptional accomplices. As such, I have deemed you worthy of wielding two of the fabled Elements of Discord." He stated while grabbing necklaces in the shape of a Bit and a Lightning Bolt. "To you, Silver Standerd, I bequeath the Element of Greed, and to you Zig-Zag, the Element of Malice. Trixie currently posses the Element of Dark Magic." He continued while giving them the necklaces, then turning to Trixie, who had one of her own in the shape of the crescent moon.

"Once we gather the other Bearers, we shall crush Twilight and her friends, overthrow the Royal Sisters, vanquish The Doctor and transform Equestria into the capital of an eternal empire!" The Master declared. "Dominion over all time and all space! Absolute power FOREVER!"

A/N: The psychic headbutt was used in the Doctor Who episode "The Lodger" to transfer a large amount of information into a human mind.

Next time!: Following The Master's escape, Twilight, the Elements and The Doctor follow the evil Time Pony's tracks, and discover a sickening experiment. As The Master tries to cover his tracks, can our heros defeat him, or will they fails to escape THE MIND OF EVIL!

P.S. The chapter titles are names of actual Doctor Who episodes, with a little pony themes tweaking here and there.

The Mind of Evil

The distinctive hum of a TARDIS fills the air as the blue barn appears alongside a red brick wall. Twilight steps out first, levitating a piece of paper in front of her face as The Doctor and the others file out behind her.

"Alright everypony, the files we found at the circus state that this is where The Master was collecting souls at." Twilight explained. "We need to find some kind of inhabited loca-OUCH!" Twilight abruptly stopped talking after walking into a sign, one attached to the brick wall the TARDIS had parked next to.

"Sunshine Valley Royal Institute for the Criminally Disharmonic?" The Doctor read. He then glanced around, confirming this to be the only building in a bright field of rolling green hills. "Well, let's have a look then."

"Hey, can I go with you guys?" Called Spike from the TARDIS doors. After the bit with the Auton Royal Guards, The Doctor had persuaded Twilight to bring Spike with them, in the event a letter needs to reach the Princess quickly.

"No Spike! We don't know if The Master is about, it's too dangerous!" Twilight Sparkle called back, causing Spike's shoulders to sag in disappointment.

The Doctor stopped for a moment. "Spike, we're giving you a very important job. Should something go wrong, you'll need to signal the Princess immediately. We're counting on you!" He assured, causing Spike to salute the group and head back inside.

Meanwhile, Rarity was knocking on the guard post by the gate. The iron window plate slid back and a security pony stuck his head out. "Can I help you?"

"Yes, yes you may. I am Rarity, and these ponies are my friends. We would like to enquire as to what..." At that moment the guard did a double take, and slammed the window plate shut. Rarity was aghast. "How dreadfully rude!"

After a few moments of silence the gates swung open with a creek. The seven friends exchanged looks, then trotted in at a wary pace. The path from the gate lead up the road to a garishly rainbow painted castle. When the group reached the doors, nobody wanted to go up and knock, so they all stood around awkwardly for a moment.

Suddenly, the doors exploded and a widely grinning Earth pony with a yellow coat and white mane. On her flank was a grinning red sun. "Hello Twilight, Rarity, Fluttershy, Rainbow Dash, Applejack, Pinkie Pie! Welcome to Sunshine Valley, I'm Happy Thoughts! I'm glad you could finally make it! Please, come inside, come inside!"

Everypony exchanged confused looks, but The Doctor motioned for them to follow her anyway. With some reluctance, the group trotted in.

"We've sent letter after letter to Princess Celestia requesting a lookie at the Elements for some time now!" Happy Thoughts explained as the eight ponies trotted down the sterile white halls. Ponies in labcoats would sometimes pass them by. "Now, has Celestia briefed you on what we need to know?"

"Uh... She told us you would be studying the Elements, but said the details would be better explained by the brilliant staff at Sunshine Valley." Twilight Sparkle improvised.

"Oh, isn't that flattering!" Thoughts giggled. "Well, I should first explain this whole place to you. As you know, Equestria is a harmonious kingdom, but even in Celestia's wonderful world, some ponies experience misfortune. This can make them bitter and resentful towards their fellow ponies. We at Sunshine Valley help them exist in harmony with their pony kin once again!"

By now, they had arrived at Happy Thoughts's office. The Bearers and Doctor stood about the room while Thoughts sat at a desk. Before she resumed dropping exposition, she activated an intercom. "Will Chief Researcher Mega Bite please report to the Administrator's office? The guests we've been waiting for have arrived!"

Happy then turned to her guests. "In a few minutes you'll meet the stallion who's gonna save the world! His work on healing disharmonious ponies has made leaps and bounds in recent months, ever since that scientist from Canterlot started assisting him. He believes that if the magic of the Elements can be replicated, we can..."

"BANISH CHAOS FROM EQUESTRIA FOREVER!" Boomed a voice as the office doors swung open. Through the doors wheeled a mechanical apparatus (a wheelchair was what it began as, but it has been heavily modified to fit its owner) carrying an obscenely fat pegasus. His coat was a withered green, and his mane was simply non-existent. Appropriately, his cutie mark was a cookie with a huge bite removed. His shriveled up wings barely peaked from beneath the rolls of fat.

"I see Princess Celestia has finally granted us an interview with the bearers of the sacred elements. A glorious day, one that will be unique in the history of Equestria!" Mega Bite exclaimed before wheeling to the window. "For too long, the sun blessed lands have been overrun by chaos and its harbingers. The release of Discord is a mere symptom of Equestria's growing sickness! Raging Griffons, greedy Dragons, jealous demon princesses, and the Windingoes are still out there somewhere! But with your help, we shall end it!" He finished while facing the group again. His eyes narrowed at The Doctor. "And who might you be?"

"I am a Scientific Advisor to the Princess, here to evaluate the faculty and chaperone the Elements." The Doctor lied on the spot, flashing the psychic paper to back it up.

"You are not permitted in this facility. Had you announced your arrival ahead of time, you may have received clearance. The only reason you six are allowed into our facility is the extraordinary nature of our research." Mega Bite spoke in a cold tone. "The orderlies will show you out."

"Now hold on just a minute. You can't just go and kick me out! I'll report this to the Princess, then we'll see where your research go..."

"Doctor, I really think you should just do as he says." Twilight cut in. "We're grown mares capable of handling ourselves, and I'm sure Spike could use some company."

"If you need a place to stay, Sunshine Valley can lodge you in the Sunshire Inn. It's a very pleasent town just down the road." Happy Thoughts added in.

"We can handle this Doc. What's the worst that could happen?" Asked Rainbow Dash, guaranteeing something awful would happen during their stay.

"Alright then, I guess I'll be off." The Doctor sighed. He was somewhat comforted by the fact that the two Institute ponies were no physical threat, and that perhaps by leaving he'll draw The Master's focus away from his friends. Still, the idea of leaving them alone while the mad stallion was loose was unsettling.

"I'm glad that is worked out. I'll have someone phone the Inn and book you a room, on us." Happy Thoughts spoke. She then gave a face splitting grin. "Okay! Before we get down to the hard science, how about a tour!" She exclaimed while leading them off.

After watching everypony depart, Mega Bite rolled away. He eventually came to a stop in the midst of a corridor. A few moments of waiting later, none other then The Master trotted from a congruent corridor. "You were correct Metal Master. The Doctor you warned me of has arrived to foil our glorious research! He even dared to fool me with his psychic paper! The mental safeguards you imparted to me proved sufficient though, and I saw through his treachery!"

"Yes, I was listening in on the entire conversation." The Master replied. "We must move quickly, lest they spoil our work."

"The Doctor is traveling to Sunshire with Twilight Sparkle's disgusting dragon familiar! To think that a student to Princess Celestia herself could associate with such a chaotic life form!" Mega Bite raged. "It just proves us correct, Metal Master. No mortal is fit to wield the power of our Goddess!"

"Don't let such things concern you, sir. I'll send some of our prototypes to eliminate The Doctor." The Master assured. "I will eliminate the Bearers myself. All you need to do is continue converting the prisoners."

Meanwhile, Happy Thoughts had led the Mane Six to a long corridor with plexiglass cells lining the walls. Trapped in the cells were a variety of dazed, expressionless ponies. "And these ponies are the recipients of the new harmonizing procedure developed by Mega Bite and the new researcher from Canterlot."

Her natural empathy triggered, Fluttershy approached the nearest cell and saw its occupant, a bony unicorn mare with a blazing flame cutie mark. The pony was curled under her cot blankets, shivering from a seemingly imagined cold. "What happened to these ponies?"

"Yes, they don't seem very enthusiastic about their treatment." Rarity observed while watching another dazed pony licking the floor.

Twilight had just finished scanning one pony with her magic. "If I didn't know any better, I'd say these ponies have had their souls stolen!" She accused.

"Well that's because they have!" Happy Thoughts declared with a cheery grin.

"WHAT!" Was the unanimous declaration from the Elements.

"Alright, hooves where I can see 'em!" Rainbow Dash ordered while getting in a fighting pose.

"How could anypony do such a terrible thing?" Asked Fluttershy.

"Oh, don't worry, they're perfectly fine!" Happy Thoughts declared in a pleasent tone. "The new procedure invented by Metal Master and Mega Bite only takes the evil part of a soul. The procedure is very tiring though, so we need to keep them here for a few days before release."

"Did you just saw old fatty no hooves has a pardoner named Metal MASTER?" Questioned Applejack. "I reckon we ought to meet this pony."

"Well certainly! Right this way!"

While this was going on, The Doctor and Spike were walking about Sunshire. The Doctor was wearing a white shirt and hat with a red trim to both of them, and a piece of celery attached to the lapel. Spike, who had on a panama hat and was carrying an umbrella with a question mark on the handle, had stumbled across The Doctor's wardrobe while he was alone in the TARDIS, now safely parked inside their quarters at the inn. All The Doctor's rather stylish outfits were too big for the baby dragon, so he got to wear the hat and umbrella, while the Time Pony was convinced to pull out one of his old outfits.

"So, have you tried dressing up as a Roman?" The Doctor asked the dragon. "Mares like Romans."

After checking in to the inn, the two had decided to examine Sunshire. It was a pretty town, full of flowers and butterflies and smiling ponies, yet something was a miss. The townsfolk seemed nervous around them, answering quickly but accurately when asked questions. Suddenly, The Doctor stopped. "Spike, stop. Can you here that?"

Spike strained his ears for a moment. "Is that... Crying?" Spike asked.

"The crying of a child." The Doctor stated in a serious tone. "And no one seems to be doing anything about it. That changes now." The Doctor rushed off towards the noise, with Spike trailing behind, one claw gripping his umbrella, the other his hat.

The source of the noise was a little Earth filly, with a slick gray mane and water blue coat. She was too young to have a cutie mark. The strangest thing about this whole scene though, was that none of the villagers seemed to notice her. They all did their best to make it seem like they couldn't see or hear her.

"Hello there!" The Doctor greeted, putting on his most cheerful face. "I'm The Doctor, and it appears to me you have a case of sorrow. Would you like to talk about it?"

The filly composed herself for a second. "I'm not supposed to talk to strange adults."

"Well then, I'll turn things over to my assistant, Nurse Spike." The Doctor replied while taking a step back. "He's a baby dragon, you know."

"I'm not a nurse..." Grumbled Spike, before he looked at the crying fily. "Um, hi there, I'm Spike, the baby dragon. I know you're pretty sad right now, but do you want to be friends?" He asked while extending an open claw.

The filly stifled her nose, wiped her eyes, then looked at Spike with wide eyes. "So... So dragons are real? You must come from really far away." She stated with awe.

"All the way from Canterlot!" He stated proudly.

The filly gasped. "Canterlot? That's where God lives! I've always wished daddy could take me there someday. But he told me nopony can ever leave Sunshire, because God and her angels in the Valley need us here." Tears began to fill her eyes again. "Daddy..."

"Where is your Daddy?" The Doctor asked.

"He went to work in the sewers last night, plumbing's his special talent, but he never came home." The filly explained. "His name is Drainy Day, and his cutie mark is a pipe with a cloth wrapped around it." Her tears stopped for a moment. "Are you going to bring my Daddy home?"

"Yes. Yes we are." The Doctor stated assuringly, causing the filly to smile a little bit. "Don't you worry..."

"Sunshine." She stated. "My daddy told me he named me that because ever since mommy went away, I've been his sunshine."

"I'll bring your daddy home, Sunshine." The Doctor restated. "I promise. Come along Spike, we've got some sewer searching to do!"

"Right behind you Doc!" Exclaimed an eager dragon. Unbeknownst to them, a shadowy figure is watching them from a window.

"Alright, this looks like a good spot." The Doctor stated, having found a secluded stallion hole to the sewers. "Now Spike, wait here for a moment. I'll drop down first, then you climb down when I give the all clear. We can't risk you getting too wet, or else your fire might not work, and I have the distinct feeling we may require a little firepower during our quest."

Spike nodded as The Doctor dropped into the sewers. Less then a minute later, a voice cut the air. "YOU THERE!"

Approaching Spike was a pair of unicorn ponies, distinguished as police officers by their vests and hats. "Just what is going on here?"

Spike giggled nervously. "Top of the morning, officers?" He greeted nervously while tipping his hat at them.

"It's afternoon." One of them stated simply before nodding to his partner. In a flash, Spike was bucked in the head, sending his hat and umbrella flying. Dazed but not out, Spike got up to charge them, only to run in place for several minutes before realizing he was handcuffed to a vertical water spout. After realizing this, he fell on his rump in defeat.

"Alright, the brat's secure. Head on down and finish the blood traitor." One commanded, causing his partner to descend into the sewer. "Now, to deal with you, lizard..."

As the second cop turned around, he found Spike free of his cuffs, hat on his head and umbrella in his grip. While the two were distracted, Spike breathed a tiny ember into the keyhole on the cuffs, melting the locking mechanism and freeing him. "Have at you, knave!" He shouted, thinking back to the knightly romance novels he reads in his quest to win Rarity's heart, wielding his umbrella like a sword.

Scowling, the unicorn used his back hoof to break a nearby window, then levitated the glass shards with his magic. In an instant, the razor glass was sailing towards Spike's face...

...Only to bounce off the thick dragon scales harmlessly. "Heh, that tickles." Spike giggled. Growing angry, the malicious police pony charged the baby head on, nostrils snorting.

Spike jumped to the side, then flipped around his umbrella, grabbing it by the end. The clever dragon then swung it in an arc, catching a pounding hoof on the question mark shaped handle. The stallion lost his hoofing, tumbled head over hooves and landed on his head. As he staggered back up, Spike finished him off with a swift umbrella blow to the head. He took a moment to adjust his hat, then went over to the stallion hole.

Flames were dragged out of his throat by self preservation when he saw a police hat rise from the sewers, but he swallowed it when it was revealed The Doctor was wearing the hat. "Be careful Doc, I almost roasted you!"

"Ah, Spike, good to see you've delt with your assassin!" The Doctor said while shrugging off his near injury. "Come on down then, I've subdued the other miscreant."

After using that officer's pair of handcuffs to restrain him, the two dropped into the sewers. The sight that greeted them was the other officer trying to get on his hooves, but slipping on the... Wet substances one finds in a sewer.

"Hold on there mate, I don't think you'll be going anywhere until you answer our questions." The Doctor spoke as the unicorn tried to swing a hoof at him. The Doctor simply reared up, grabbed the oncoming front hoof with two of his own, and using the chumps own weight to slam him into the wall.

Spike looked dumbfounded. "Where did you learn to do that?" He asked.

"Venus." The Doctor replied simply. "Now then, how about you answer our questions?"

"Never. I shall not betray God. You and your mud lizard might as well soak your head in this filth, might make you feel clean." He stated back between pained wheezes.

"You know, I don't like your attitude, and I don't think we're gonna get much from you." The Doctor replied. Then, in the most nonchalant tone possible, added "Spike, roast him."

"WHAT!" Exclaimed the police officer.

"WHAT?" Exclaimed Spike.

"You heard me. He's obviously not going to give us anything, and I'm rather put off by his attitude." The Doctor explained. "None of that teleporting magic, by the way. Extra crispy."

"You're mad! You'll get life banishment for murdering a police pony!" The officer exclaimed.

The Doctor huffed. "Any place I could be banished to would be dust in four ticks of a Time Ponies hear, long before my life is over." He turned to Spike. "Are you going to fry him or not?"

"Wait, wait! I will do God no good dying here, and it matters not what you know." The police pony finally cracked. "What do you want to know?"

"Where is the little filly's dad, Drainy Day?" The Doctor asked.

"Drainy Day..." The officer growled. "He was always a troublemaker. Had dreams of leaving, when the great Celestial plan requires everypony in Sunshire to remain here."

"If you have murdered him, I assure you..." The Doctor began to threaten, real rage building up inside him. Though he had been bluffing when he ordered Spike to kill him, if he were to hear that this pony had made that little girl an orphan, he might very well make good on his threat.

"No, Drainy Day isn't dead, he is more alive then any of us." The officer added quickly. "He has been taken by the angels."

The Doctor's face grew pale at the mention of angels. "What kind of angels? Where do they come from?"

"Holy angels, built by the Institute... They require sacrifices..." He wheezed out. Suddenly a crimson red laser seared through the air and struck the pony dead. "Spike, dodge!" The Doctor exclaimed as the duo avoided several more shots.

Harsh mechanical hoofsteps could heard as a gleaming silver figure in the shape of a pony emerged from one of the sewer tunnels. The Doctor's eyes went wide as he recognized it.

"A cyberpony..."

Meanwhile, inside Sunshine Valley, Happy Thoughts has lead the Mane Six into a dark room. "This better not be a trap!" Threatened Rainbow Dash, but when she turned to where the administrator was standing, the perky pony was gone. The six then heard the door lock behind them.

"I reckon this is trap, Rainbow." Applejack stated.

"SURPRISE!" Came a yell as the lights went up, revealing the Six to be in an operating theater. In the viewing seats above them, The Master and his three cronies, Zig-Zag having been the one to yell surprise. "Is everypony ready to die?" She asked with a psychotic grin.

"Now Zig-Zag, do try to contain yourself. I prefer to think of this as a healing exercise." The Master took over. "Once we use the negative thoughts we collected from these miscreants and murderers as we stole their souls- splendid bunch, by the way- these little ponies will have a much finer understanding of their less... acknowledged sides." He turned to Silver Standerd. "Throw the switch."

"We should just gas them..." The Element of Greed muttered while throwing the switch. The lights below went from white to red as our six heroes were suddenly split with headaches. The world began to go dark as evil consumed their minds...

Inside Twilight's mind, the purple unicorn stood in the burning remains of Celestia's palace, the Sun Princess at her feet and the moon above her head. Nightmare Moon stood beside her. "Well done, my apprentice. As Equestria's new Queen, I decree that you shall be granted all the magic knowledge in Equestria!"

Within Applejack's mind, she saw herself, Apple Bloom and Big Macintosh cornering a cowering Golden Harvest. "Now how many times has mah big sister gotta tell ya? Ponyville is an APPLE town, so keep your cotton-picking carrots to yerself!" Her little sister shouted.

"Eyup." Her big brother added.

"Now, let's see if mah special talent is breaking kneecaps!"

Pinkie Pie's dark fantasy was of her in a big city alley, trading a bag of pills for a handful of bits with a shady looking pony. "Thanks Pinkie! Me and my crew are gonna party tonight!"

"Enjoy the rush. I'm just glad to get of my boring family farm."

Inside Rainbow Dash's mind, the pegasus was walking down the streets of a seedy looking neighborhood. In this fantasy scenario, her wings were crumpled up against her back, smashed flat in an accident. "Hey Rainbow Crash!" Called a rough voice. "How're the wings doing?"

In an instant the aggressive pony had charged across the street and was brutally beating the heckler within an inch of his life.

Fluttershy continued to see darkness, however the sound of tiny hooves reached her ears. Upon hearing it, a blind, flightless Fluttershy, moving through memory, arrived on the porch of her isolated cottage. "HEY YOU LITTLE RATS, GET OFF MY LAWN!"

Rarity was seeing herself inside a jewelry store, a home made mask on her face, her magic pointing a knife at the clerk. "Give me all your gemstones or so help me I WILL CUT YOU!"

Across all their minds, they could hear the evil laughter of The Master.

A/N: The Doctor is clad in his Fifth incarnation's garb, and Spike's accesories come from his seventh.

This story really does have more in common with Attack of The Cybermen then The Mind of Evil (The bit with the police officers was right out of AOTC) but we still had prison brainwashing, so I titled the chapter Mind of Evil to avoid spoiling things.

The character of Mega Bite is partially based on recurring Doctor Who villain Davros, which is he why he distrusts him.

Also, if anyone here is familiar with TvTropes.Org, could you please inform me if they accept Fan Fiction? I'm curious if they would take a page on my story. I figure it would be a good reference page for any readers unfamiliar with the Doctor Who elements.