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!