Return of the Master

by Dusty Old Qrow

Rating: teen
Tags: Crossover, Adventure
Length: 17460

Something has gone wrong with the TARDIS, causing the Doctor, Derpy, Twilight and Spike to remain in Equestria. Meanwhile, Jack Harkness has made his way to Equestria, to aide the Doctor in a battle that will shake all of Equestria!

Currently under indefinite hiatus!

Set in the same Universe as The Weeping Gardens and takes place directly after, but you don't need to read that in order to understand this. There are only a few subtle hints linking the two.

The Doctor's TARDIS malfunctioned. It died, in a sense. The soul of the TARDIS has gone.

And now, the Doctor, Derpy, Twilight and Spike remain in Equestria, just as Jack Harkness makes his way to the Pony-Verse, in order to aide the Doctor in a fight that will surely shake all of Equestria.

Co written by Dartrunner!

PLEASE NOTE: THIS IS NOT DISCORDED WHOOVES. I AM ONLY USING THE DESIGN OF THE DISCORDED DOCTOR FOR THE MASTER.

Published 1970-01-01 00:00:00 UTC
Last updated 2013-12-17 02:58:04 UTC

Still in Equestria

The TARDIS shook and sputtered, sparks flew, causing the Doctor to stumble away from the controls, knocking over Spike, who ran into the console, making matters worse. "Augh!! Somepony's been messing with my TARDIS!!!" The Doctor screamed. Flipping switches and pushing buttons, the Doctor tried with all of his might to stop the machine, but nothing he tried seemed to offer up any results.

Derpy ran into the Doctor, knocking him off of his hooves, over the side and down to the area underneath the console.

Then, the shaking stopped.

"Oof... Everypony OK? Ow... I think I hit my head..."  The Doctor said, getting a yes from all three of his companions, Spike the dragon, Twilight Sparkle and Derpy Hooves. "Don't touch anything... I'll come up in a second..." The Doctor said as he sat up, and stood on his four legs. "Now then! Why are you making all that ruckus, huh?" The Doctor said as he took out his Screwdriver and rushed up to the console.

"What was that all about?"

The Doctor scanned the console, and found no damage. "Huh..." He scanned more parts of the console, with each time getting more of a confused look on his face. "That- that's not possible. No. No. It-it's dead! The TARDIS is dead... The last one in the Universe..."

"What- What do you mean, it's dead?!" Twilight asked, running up to the brown stallion, who had a grim look on his face. "Are we stuck in Equestria? Not going to your Universe?! What about reality?! It's gonna blow up!!"

"Twilight, there's nothing in this Universe to distinguish the Time Vortexes. They've separated, gone into their respective places. Mine's gone, so no, reality won't blow up." The Doctor laid a hoof on the TARDIS’s console, and shed a tear. "The last TARDIS..."

"Um... Twilight, who is pony? You have't given me a straight answer ever since we met him!" Spike asked for the second time in the TARDIS. Twilight looked to the Doctor for an answer. She had virtually no idea who he was, other than that he was an alien from another world who saved people. The Doctor only once talked about his past, and never mentioned it again. Twilight wasn't sure if Derpy knew who the Doctor was.

"All you need to know, Spike, is that it doesn't matter anymore. The TARDIS is gone. I have no reason to stay in this town, now. But, because I have friends here, I'll stay around for a little! Oh, I'll need a name... 'John Smith' isn't really a name you hear around Ponyville very often... Oh! I got it! 'Time Turner'! Ha ha! It's better than 'Random Pony Who Travels Through Time' isn't it?" The Doctor continued on one of his annoying, yet charming, rants that no pony understood.

"Anyway..." The Doctor said, straightening his bow tie and clearing his throat. He took a quick look around the dark console room, and turned to his companions. "Let's see if we've moved, shall we?" He said with a grin.

The TARDIS doors opened with an audible creek, as the Doctor poked his brown head out from inside. He looked around to discover that that they are still in Ponyville, but have moved out of Twilight's library. They were in the center of town, no pony paid attention to the blue box that had appeared out of nowhere. Stranger things had happened in this town. Nightmare Moon, Discord, Heck, even the Hydra itself! Nothing scared these ponies anymore.

So no pony paid any attention to the strange blue box that had appeared with a loud noise.

The Doctor stepped out of the TARDIS, once again straightened his bow tie. "Blasted thing... Always coming out of place... Anyway! Ponyville! TARDIS! Something wrong! Investigate!" The Doctor said, giving a slight jolt and then continued through the town square. It was much like the rest of Ponyville, save for the town hall and a statue of Mayor Mare, thankfully no longer a Weeping Angel.

Twilight and Spike then came out of the TARDIS, followed by Derpy, who all looked around to find they were in the Ponyville they knew and loved. "TARDIS is dead... Can't go out and see the universe. I've been here far too long, possibly a day or two late... Wouldn't have worked if I tried to re-power it with my life force. My body has grown accustomed to this form... Stuck in this Universe forever. A Time Lord without access to Time. Like taking a Pumpkin out of its patch."

The Doctor closed his eyes, and sighed. "Well, come along, friends. We have some investigating to do."

Darkness...

The Doctor's ears pointed straight up in the air. He had heard a voice... a raspy, whisper.... "I-it's nothing... J-just... Time Lord jitters?..." He tried to assure himself.

One...

"!!" The Doctor took out his Sonic Screwdriver and pointed it directly at Spike, causing all of his companions to stagger back in shock. The Doctor then pointed the Screwdriver to Derpy, then Twilight.  "Augh!" The Doctor's body contorted, making him drop the Screwdriver and grunt in pain. His friends rushed to his side, Twilight picked up the Screwdriver and put it in the Doctor's collar. He may not wear a shirt, but he wears a tie.

Two...

"AUGH!!!! I need to get inside!!!" The Doctor screamed.  Twilight picked up the Time Lord and escorted her friends to the Library, the Doctor still screaming in pain.

Three...

The Doctor rested in Twilight's bed. He had a very high fever, and constantly had violent spasms of pain. When the Doctor was conscious, he had told them that he was not regenerating, but something was extremely wrong. If they did not resolve this quickly, then something would obviously go wrong. It is the way the Doctor's life was. Doctor is down, aliens invade. It is like the universe had something against him...

Four

The Doctor has gotten slightly better in the last few hours, but not much. The spasms have been less frequent, and his fever has gone down, though he hasn't woken up yet. Derpy says not to worry. "He's the Doctor," She had said. "He's been through worse and been back in time for muffins. He'll be fine." Though, Twilight wasn't too sure. Spike was really disappointed. He hasn't gotten a taste of what it's like, travelling with the Doctor. Everypony else has!

Twilight was laying in the spare bedroom in the basement of the Library, thinking not only about the Doctor, but also about the TARDIS, which had been left in the town square to waste away and rot. It was already dead, no use keeping it. As Time moves on, it'll be buried. Derpy said he's tried that before. She flew it back to him. How? Twilight had no clue, she hadn't asked. And it didn't matter anymore anyway. The TARDIS was dead.

Like she needed reminding.

"Augh... H-hello?... Where am I?" The Doctor asks, staring into a black void. He could feel ground beneath his hooves, and even felt wind on his face, so he knew he was somewhere in the physical world. "I- My name is Time Turner..." The Doctor says to nobody. What was he doing, talking to himself? Nopony was here, he should just walk away and get back to Derpy, Spike and Twilight.

So, why didn't he?

It was possibly the adventurer within him. The excitement of the unknown. The lust for mystery. It was so great, yet so terrible. He should walk away... Walk away... Walk away...

But why? No harm in finding out where I am.

Your friends would be worried.

.... What?! Wh-Who are you?! Get out of my head!!

I'm not in your head. I'm a figment of your imagination.

Yeah, well I was Amelia Pond's imaginary friend until I showed up at her wedding. How do I know you're not somepony wanting to take a physical form?

Well, you're not at a wedding. That's different.

... Well played, voice in my dreams. Who are you?

....

Not going to tell me then, huh? Well... I guess I'll have to find out by myself...

Spike went for a walk. The sun was setting, so it wasn't completely dark out, though if he went too far from home he would need to hurry. He wasn't scared or anything, but Twilight would start to worry, and he didn't want that, with the Doctor being bedridden with some sort of super freaky Time Lord sickness or whatever. Spike didn't entirely trust the Doctor, but if Twilight trusted this guy, it was good for him.

Kind of.

Sure, he didn't really have a choice not to trust him, but he didn't.

He walked into the town square, the dead TARDIS only a few feet away from him. He walks over to it, and opens the door with an audible creek. He looks around the dark console room, and walks in. "So... The Doctor had those adventures in here..." Spike says, and goes up to the controls. He puts his hand on a button, and slowly presses it down.

Nothing happens.

Spike sighs. Hunk of junk.

Then, Spike grins.

He rushes to the controls, pressing buttons and imitating the sounds of lasers firing. "Commander, we're hit!" Spike says in a deep voice. "Set the shields to high! Starlit, man the blasters!" Spike says, now in his normal voice. He presses buttons and flips levers, making different voices, with his normal voice being the leader. He then makes an explosion-like noise, and shakes the console.

"We're going down! The alien scum is too strong-!"

"Well, well, well, look who it is. Pretending to fly the TARDIS... How cute..." The voice sounds familiar, but different. It was a Stallion's voice, that's for sure. Spike turns around to see the outline of a medium sized Stallion, just taller than Twilight or Derpy. "Looks like you need to know... Never... Touch.... The TARDIS..."

"D-Doctor?!"

The Stallion laughs. "No."

"Call me... The Master..."

The Master

"The- the Master... Doctor, what's gotten into you?!"

"I told you, I'm not the Doctor..." The Master walks over to Spike, and looks at him. "Why would the Doctor chose you as a companion? Pft. They're getting younger every time."

"H-hey!"

The Master turns away from Spike, and the moonlight finally allows Spike a good look at the stallion. He looked exactly like the Doctor, straight up to the hair style, granted a bit more messy, but instead of a green tie, he had a black Bow tie. His coat was grey, and his eyes were a cold, ice blue. Also unlike the Doctor, he was a Pegasus. His wings were nearly the size of Celestia's, if not smaller. When he looked at Spike, he went cold. The Master was definitely not friendly.

"Tell the Doctor this," The Master says, looking back at the purple dragon. He grabs one of Spike's spikes, and hold him up to his face....

The Doctor gives a loud, agonizing scream, the cause of which unknown, but yet he screamed. He screamed for about two minutes, before he calmed down and opened his eyes. "Well... That Ood- er- odd..." The Doctor says as Twilight rushes into the room, and sees the Doctor. She walks up to him, and lightly taps him on the shoulder. "Um... Yes, Twilight, I'm real... No need to act like a certain someone...."

"D-Doctor... You're alive... And you didn't regenerate..."

"I wouldn't say that. This body, my eleventh, has been in use for over 400 years... I still need to face a prophecy... 'The fall of the Eleventh'..." He looks out the window to the town square, where the TARDIS sits. He closes his eyes and sighs. "Something's wrong. Derpy!!!!" The Doctor rushes out of the bed, and drags Twilight along with him to where Derpy was sitting in the living room.

"D-Doctor-!"

"Yes, yes, I'm alive. C'mon! Something's wrong! Come along, mares!"

"Doctor!" Derpy shouts as the Doctor puts on his tie, placing the Sonic Screwdriver in the collar, and dragging his companions out the door. "Doctor, what the hay is going on?!" Derpy asks. The Doctor runs to the TARDIS, and fumbles with the key, which falls to the ground. Twilight sighs, and places the key in the lock, and opens the door. The Doctor thanks her, and rushes in to find a puff of smoke flying out behind them, and little Spike laying on the floor.

"Spike!!!" Twilight gasps. She runs over to her friend, and checks his heartbeat.

There was none.

"No!! Spike!! Doctor, do something!!!" Twilight begs the Doctor, who rushes over to Spike and scans him with the Screwdriver.

"Get him to the Zero Room. We can still save him."

Twilight rushes to get Spike levitating, and looks to the Doctor. "Follow me." The stallion says, and rushes ahead of Twilight, who runs after him. "Derpy! Keep watch in case something goes wrong!" The Doctor yells as he runs and turns to the left, stops, and turns around. "Wrong way!" He yells, half laughing and half mumbling in embarrassment. "The Zero Room should be just beyond the pool, and across from the Billiards room!"

"Look at the small Doctor... Rushing around in his little blue box trying to save his friend... It's too late now, but he can try." The Master gives a small laugh. He was flying above the console room in the TARDIS, hiding among the shadows. The new grey coat helped, of course. Some parts of this new pony form was borrowed from ponies that the Doctor came to know from his time in Ponyville.

Derpy's grey coat, Celestia's wings, though the fob watch Cutie Mark, that was his own doing. He had taken form from the Doctor's dark side, much like the Valeyard, though he is not the Doctor.

The Master floated down, barely making a sound. Derpy didn't hear him, not even turning around. He slowly walked up to her, the moonlight reflecting off of her grey coat and blonde mane. He understood why the Doctor took a fancy towards her, though, personally, he can do better.

He was now right behind her. He taps the grey mare on the back, causing her to jump and turn around. Thanks to her shadow, the darkness of the console room and his grey coat, she barely saw a difference between him and the Doctor. The Master kept his wings close to his body, and made sure to keep them hidden. "D-Doctor...? When did you... How did you...? What?"

Derpy looks to the stallion.

And he laughs.

"Let's see how the Doctor fares with only a bookworm to rely on..."

Not Again! (Written by Dartrunner)

"This way!" the Doctor shouted as he ran down the TARDIS's various hallways with Twilight.

"Here!" He fumbled with his Screwdriver in an effort to open the door leading to the hallway, leading to the Zero Room.  The door did not open on command so the Doctor forced the door open with a grunt.

Panting, he stumbles through the spherical room toward the far wall, trying to open a panel that activates the Zero Room

Remember...

"Gaahhh!!!", the Doctor shouted as he fell on his side.  His fore-limbs wrapped over his head, he curled slightly inward.

"Doctor!" Twilight shouted as she enters the room, gently setting Spike down in the centre of the room, and quickly kneeling by the Doctor’s side.  Not sure what to do, she simply watched, overwhelmed by what was happening.

Remember...Remember who you are...

The Doctor, still gripping his head with one hoof, pushed himself into a slouching position  against the wall.  "Twi...Twilight, do...do you know any... ahhh!! My head! Know any healing or...or pain tol...tolerance spells?!"

She shook her head, too distraught to speak.

"Then I guess it's... it's willpower..."

Barely breathing through the pain, the Doctor relaxed and closed his eyes.  Cringing as the voice came back.

Remember what you have done.

Muttering to himself: "Not a good time voice in my head," he controlled himself, calmed down, and stood.

"Doctor!" The Doctor turned to Twilight. "Are you alright?"

"For now, I still feel some pain, but I can manage.  But this is not important right now, Spike is."

He turned back to the wall, and searched for the panel. Then he realized his error."No. Nonono!"

"What, Doctor?!"

"NO! Not now! Not another!" he turned back to Twilight.  "I can’t save Spike, not without the TARDIS, and since it is dead, there is nothing I can do for Spike! Not another one!!! Spike!!!"

"You must!"

"I’m sorry! I’m so, so sorry..."

Twilight went and laid down next to Spike, pushing her muzzle into his chest."Good bye, Spike... My number one... fateful assistant..." Twilight cried next to her friend. The Doctor trotted up to her, and placed a hoof on her back.

After a few minutes she stood, through tears she choked out,"What now?"

"Without the TARDIS I can’t save Spike. If we had a way to preserve his body, I could save him.  But only if I can restore the TARDIS."

Sniffling, Twilight spoke,"There was a preservation spell I read about in one of the books in my library."

The Doctor managed a slight smile from watching Twilight regain hope."Then let's go, the more time we waste, the harder it will be to bring him back!"

All of the sudden, a blood curdling scream echoed throughout the TARDIS.

“DERPY!!!” The Doctor looked toward the door, and started to hobble to the control room.  Twilight, still whimpering, picked up Spike and put him on her back and turned to follow the Doctor.

Run, Doctor... Run, like you always do... And every time, someone dies. Who will it be today, Doctor? Ditzy? Twilight? Spike? Or maybe you. I never know, nor do you. It’s strange, fate. You never know what’s going to happen.

“Who... Are... You....?” The Doctor mumble, and doubles over in pain, causing Twilight to trip over him, dropping Spike’s body, which goes flying down the hall, landing with a thud. “Get... Out... Of... My... Head...” The Doctor mumbles.

“Doctor! Get up!”

“Go... Twilight... Go...”

The purple unicorn looks to the Doctor, and picks him up with her magic. “Not without you.” She picks Spike up, and runs through the halls the the console room, where they find one less Pegasus. “Derpy!!! Where are you?!” Twilight yells.

Doctor...

I’m here, Doctor...

Here... For you...

Here for her.

Like you never were.

Hello, Derpy... (Written by Dartrunner)

Derpy woke up, laying on a couch with a blanket covering her.  She sat up and looked around the room.  There was a door, with a red glowing EXIT sign above it, about two meters behind the couch. The room was approximately 10 meters wide and 20 deep.  There were two rows of tables covered in various panels, monitors and computer equipment, with chairs scattered about the room. The couch was facing a path leading down the room, in between the rows of tables.  The far wall was plaster with large screens, all of them were off except the one in the middle.  It was the only other light source in the room besides the EXIT sign above the door.

Derpy could not see what was on the screen, as there was a pony standing in the way.  She hesitated before she spoke.

"He...Hello?"

The pony across the room turned to face her, his face obscured by the light from the screen.  As he started to walk toward her he spoke.  "Ah, I see you are awake.  Good."  As the pony approached Derpy, she could make out some details.  The voice told her it was a stallion, he had a dark grey coat, a black spiky mane, and a similar build to the...

"Doctor?"

"Ha!  Yes...and no. A bit of both, actually."

She looked at him in confusion, still unable to fully see the stallions features.  "Who are you then, if you are not the Doctor?"

"Oh! But I am," he spoke, cutting her off before she could ask anymore questions. "I am a bit of all of you." He stepped forward as the light above him flickered on.

"I am the manifestation of, the Doctor," spitting the name out, " and his...companions."  He stopped to study her for a moment, seeing how she reacted, how she felt about her friends.  All the questions that she had.

"I have parts of each of you; the Doctor's body, and part of his mind, these wings," he opened his wings, covering Derpy in shadow. "Now they are interesting, they can't be your's, they are much too big.  Although you are most likely the influence for them.  The coat, though darker, is yours.  I even have a bit of magic from the purple one and that dragon." He kick the ground with his hoof, creating a small spray of sparks. "Of course the conscience is my own.  Though, none of this would have happened without the essence of the TARDIS."

Derpy was at a loss of words, she did not fully understand what, or who, this stallion was.  Scared that he knew of them.  She had never seen him in her life.

The stallion stared at her for a few minutes, then spoke, "Come on, next question.  I know you have many, and I have things to attend to."

"Where, are we?"

"A wonderful question!  You, are in, or more accurately, under the Everfree Forest." More questions filled Derpy's head. "You are in a secret, underground, 'sanctuary'.  Though I prefer the term, 'place to hide while her empire crumbles'.  You are in a bunker, built by Princess Celestia, so she could hide from any threats she, or the Elements of Harmony, could not handle.  Some place she could hide, while Equestria was invaded, conquered and occupied; from an external force, or an internal shift of power.  She doesn't care for you! Any of you ponies that live in this country!

“She built this so she could hide, while all the ponies she ‘cared’ for died.  It was built for her and only her.  Any pony that worked on the design or construction, was... hmm...what’s the word I’m looking for...removed.  Though she has long forgotten its very existence, as it was built almost 800 years ago, during... troubled times.”

Derpy could not understand why the Princess would need to worry, “What threats would Princess Celestia have to worry about?”

“That! is not a relevant question, and besides, it is ancient history; no pony cares, or even remembers that far back.  Now, moving on.”

“Who are you?”

Annoyed the stallion replied, “You already asked that.”

Derpy looked at him, “I mean, what is your name?”

He began to walk around the couch on which Derpy still sat, “I have been called many names over the years; Koshei, Duke Dominus, and Estro... We fought, Derpy.”  Derpy had no idea what he was talking about.  “You must remember me... I was the cause of the Doctor’s ‘Regeneration’ before you three reset time.”

“You were the cause of that?!”

“Yes, I was... And I would have killed him, had it not been for my conscience.”

Derpy’s eyes widened in fear. This stallion was a potential murderer.

“You still haven’t answered my question. Who are you?”

“I am...” The stallion walks over to Derpy, giving her a clearer view of his face. It was identical to the Doctor’s, save for bags under his eyes and a grey coat.

“... The Master...”

Forever Burdenned

The Doctor lay on the floor of the library as Twilight started to perform the preservation spell, meant to kept Spike’s body protected and stop it from decaying until the Doctor could restore the TARDIS.  Twilight’s horn glowed a bright purple as she worked.  Tears still ran down her face and chest as she focused.  She picked up Spike with her magic and began to cast the spell on him.  A deep magenta glow developed around his body as he took on a fetal position, with his tail in front of him, near his head.

The Doctor watched Twilight as she concentrated, driven, empowered by the emotion that flowed through her.  After all the time he had spent in this world of magical ponies, he still did not fully understand why or how unicorns were able to perform “magic”.  Much of it could be explained through science, but somethings still eluded him.  Unicorn magic was one of the most powerful, volatile and versatile energies the Doctor had ever come across.

The Doctor was interrupted mid thought, when he had to avert and cover his eyes as a bright, blinding light consumed the room.  When he turned back to look at Twilight, she was sitting on the floor with Spike floating in a magenta coloured sphere.  She turned to him and spoke.

“It’s done...”

The Doctor moved in to comfort her as she began to cry again.  “Shh... It’s ok, it’s ok.  I can save Spike, once I fix the TARDIS. Everything will be fine, we will get through this."  He cradled her in his hooves, gently rocking her back and forth.  "For now, we need somewhere we can hide Spike, so no one will disturb him."

Derpy had found many interesting things since she started to explore the bunker.  And to her surprise, much of what that has been sitting down here for the past millennia was in fairly good physical condition.  Especially the living quarters, within them held many things to keep one entertained, whilst they hid from whatever was above.  The bed, a massive thing that felt like sleeping on clouds,  was the only exception, it had been slept in by the Master and was unkept.

The Master had let her explore so as to keep her out of his hair.  She had slept for almost a day, was hungry and constantly asked questions.  He would normally just rid himself of something that annoying, but he needed her alive and well.

The Master had directed Derpy to where she could get some food.  His directions lead her to a large room with a odd looking machine.  It was basically rectangular in shape and there was a screen on the far right side of it.  There were multiple tubes running from the machine to vats of Celestia knows what.  Derpy was told that it was called a "Nano Forge", and could create whatever anypony could desire, so long as it had access to the raw materials to build it.  The Master had explained how to use it, and then, fairly in-depth the details of the inner workings.  Derpy only caught "3D printer" and "runs on warm fusion" before she got sick of the grey pegasus, and left.

She approached the machine's screen, and hesitantly tapped it with a hoof.  She jumped as it flickered on.  A list of hundreds of items appeared on the screen, some Derpy knew what they were, but most were a mystery to her.  She tapped the food category, and scrolled through the list.  Some apples, hay sandwiches, and even gems for dragons. She was hesitant at first to scroll through the rest of the list, but she did anyway.

“I see you’ve figured out how to work it.”

Derpy jumps. She turns to see the grey Pegasus walking towards her with a tired look in his eyes. “I’m surprised. From what I’ve researched about you, you’re not the brightest of ponies.” Her eyes go wide, and she hurls a hoof through the air, only to be caught by an invisible wall. “I,” The Master begins. “Would not advise that. I’m the one keeping you alive, Ditzy Doo. You’d best not forget that.”

“... How do I make these foods? ‘Raw materials’, I don’t have any materials!”

The Master sighs, and taps the apple.  The screen changes and displays the required materials and the time to produce the item.  He taps the begin option and the machine starts to hum.

“The materials are stored in the vats, when you select something to build, it takes in what is require and assembles it on a molecular level. Use it too much, it runs out. Duh.”

Derpy tried to smack him again, but she was thwarted by the invisible wall yet again..

“I told you to stop that.”

“Why? Are you going to kill me?”

“You? No. Everypony you know? Yes. Now shut up,” The Master grabs the apple that had appeared as the side of the forge opened.“And eat.” He then shoves the apple into Derpy’s mouth. “I’m going out. Don’t. Touch. Anything, or I will kill you. Stay in your quarters, and do not try to escape. Doing so will result in death. Right then and there.” The Master turned and walked away into the main room, where he opened a little hatch and flew out, and the hatch closed behind him.

“That Pony, I swear... I wonder what he wants with me...? I’m not special, I’m not important... I’m just a klutz who met an alien time traveler from another dimension...”

Derpy continued to munch away at the apple as she looked through the rest of the list.

Plans of the Master

The Doctor and Twilight had just finished setting Spike’s body in the bed in the basement of the library, where nobody will think to look for much of anything, let alone him. “Okay, that should be it. His body is preserved, and the bed will make sure his skeletal structure doesn't bend out of shape.”  Spike laid on his back, the magenta glow still covered him.  He looked peaceful in this state.  ”All we have to do now is find a way to restore the TARDIS and locate Derpy.  Now, explain this to me, Doctor... What exactly caused all of this? Who killed Spike?  Who stole Derpy?”

The Doctor looked to the ground. He kicked at the ground with his front left hoof, and closes his eyes. “I... Don’t know.”

“Doctor. Don’t lie to me.”

“T-Twilight... Remember this: If I lie to you, it is to protect you. Right now, we are facing an enemy that even I cannot handle. This enemy is even tougher than the Angels. Remember when I told you who I was, before we reset time? I told you about the Daleks. Imagine all of the things I told you about them, and multiply them by ten thousand. I am lying to you to protect you, and for no other reason. Spike is dead because a pony out there wants to get to me and most likely kill all I care about, then end with me. And the only way to do that is through you, Derpy... and him.” The Doctor looks to Spike, and back to Twilight. “This pony... His name is the Master.”

Twilight’s eyes went wide. “That pony we fought in Manehattan? I thought the Paradox put him back in your universe!”

“No... It put his soul into my darkness... And through that, he gained life once more. He improved himself, taking the best bits from all of my companions, including you, and myself and put them into his body and mind.  He is unlike anything I have ever faced, Twilight, and you need to know: Right now, there is no way we can win with just the two of us.” Twilight looked to the Doctor. She was shocked at how a stallion so wonderful, so... brilliant, could sound so helpless.

“Doctor.... Y-you’re serious...”  She turned away from him in disbelief.  After all the stories he had told her;  About how he had saved countless lives, thousands of times.  Always giving a second change to those who deserved it.  She could not believe that he was powerless against against this foe.

“Yes I am, Twilight. As long as we only have you and I to fight him, we stand no chance and we will win. I’m so sorry, Twilight... I’m so... so sorry...”

The Master was flying through the Everfree forest, careful to make sure not to be spotted by any travellers from other towns. As he flew, his thoughts wandered from getting back home, why the TARDIS chose now to release the evil inside the Doctor, and what he was going to do the Ditzy. He knew his plans for her, yes, but as to what he was going to do to get her to be less annoying, he had no idea.

“That mare.... The Doctor sees something in her, I can’t tell... Yet, I can feel it...”

He was nearing Ponyville now, being at least 2 miles away. The sun was beginning to rise, illuminating the forest in a beautiful shade of gold-red, reflecting off the leaves and into the sky. To be honest, it reminded him of Gallifrey, the red leaves and grass. The only thing it was missing was the mountain ranges that stood proud high in the sky. But thanks to the Doctor, it was all gone.

He was over Ponyville now. He could see the Library, and the dead TARDIS in the center of town. As it was morning, there were ponies starting to wake up and go to their jobs. “Pft. Pewny ponies.” The Master says, and flies down to the center of town, right next to town hall. “Okay, Doctor... Time to see what you’ve got...” He then fires his Laser Screwdriver directly at a group of ponies, most of whom were killed instantly, they simply slumped over and fell.  While others duck behind tables or other ponies for cover.

“Run, ponies, run!” The Master laughs.

He then fires at Town Hall, setting the building aflame.

“Freeze!”

The Master turns to see a group of five unicorns dressed in blue. The Ponyville Police.

“I surrender!” The Master laughs. He walks up to the unicorns, and grabs one, throwing him into a second. A third tries to blast him with magic, but the Master rolls out of the way, and shoots him with the Laser. The fourth and fifth both rush at him, but he flies up and they hit each other, and the Master bashes their heads together, knocking them out.

Set Fire to Ponyville

The Ponyville officers laid at his feet, all unconscious, save the one he shot with his laser, whom was dead. “Now to find the Doctor...” The Master mumbled.  With a leap, he took to the skies and flew across Ponyville, firing his laser at random buildings as ponies ran in all directions. He noticed a blue unicorn mare in particular, for reasons he did not know. She did have a distinctive coat, so he chalked it up to that.

He dropped directly in front of her, causing her pupils to shrink and her mouth to drop as she curled back from him. He chuckled, and aimed his screwdriver at her.  As it began to glow, her horn started to glow as well, but before either of them could fire, a rock hit the Master in the side of the head, disorientating him temporarily.

“Run!” The Master heard through his newfound headache.

The Doctor and Twilight ran outside to find buildings set ablaze and ponies lying dead in the streets, from what appeared to be an act of terrorism. “Doctor...” Twilight turned to look at him. “I think we’re in trouble.”  The Doctor took out his Sonic Screwdriver, spun around and frantically scanned the area.

“Weird... It says I’m here... And down the street...”  He looked to where the signal came from, then back to the screwdriver.  ”It's not the first time something like this has happened...” The Doctor looked from the brown and green device to Twilight. His eyes lit up as he realized what that meant.  “It’s the Master! He's here!  We’ve got to hurry,  GO!” He said as he started to race down the street, with Twilight following close behind. “Come on, Twilight! We don’t have much time!”

“You’re not very fast yourself, mister!”  She spoke as she easily kept pace with him.

As Twilight finished, she noticed Colgate, the Ponyville dentist, cornered by... “Doctor?! How... Is that him?!” Twilight asked with surprise. The Doctor stopped with a skid, and scanned the grey pegasus.  He looked to the purple unicorn with fear and worry.

“Yes.”

“We’ve got to help her!”

“Yes, I know...”

Twilight looked around, and saw something that might help them. Her horn glowed as she levitated the small object from the ground, and hurled it towards the grey pegasus with great speed. She smiled as it made contact with his temple. “Yes! Doctor, I got him!” Twilight said gleefully, but the Doctor was not there to hear her. He had run towards the blue unicorn, and grabbed her by the hoof.

“Run.”

“Doctor...” The Master grumbled. He slowly got up, and saw the Doctor running away with Twilight and the unicorn he was just about to kill. “Oh, no you don’t!” The Master spread his wings, and flew after the Doctor, who had made it to the Library and went inside. The Master noticed that it was a tree, and smiled.  He once again took out his Laser Screwdriver, and fired at the Library setting it aflame.

“Try getting out of that one, Doctor.”  He laughed as he flew away.

“Get in, get in!” The Doctor said to the two Unicorns as they rushed into the Library. “Twilight, get down to the basement and grab Spike! Colgate, it is Colgate, yes? Anyway, stay here, and don’t get into trouble-” The Library exploded with a flash of red and orange, sending the Doctor and friends to the ground. “Take cover! Twilight! Colgate!”

The Library started to fall apart as branches, pieces of wall and ceiling broke off and crumbled. The Doctor got up from the ground and dodged the debris as he ran over to Colgate. “Get out of here...” The Doctor coughed as the smoke began to overtake the room.  “I’ll get Twilight... R-run...” The Doctor lead Colgate to the door, and opened it for her.  She turned to look at her saviour.

“Th-thank you.... Who are you?”

The Doctor gave her a weak smile. “I’m the Doctor.”

“Doctor who?”

The smile faded. “Exactly.”

The Doctor closed the door and leaned up against it for a second. “T-Twilight...” The Doctor managed to choke out the name before he enter a fit of  coughing. The smoke was getting extremely thick. It would be a wonder if Twilight was still conscious. It wasn’t effecting the Doctor as quickly as it would a  regular pony, but it would kill him eventually.

“*Cough!!* Hold on... Twilight...” The Doctor wheezed as he stumbled away from the door, which, being made of wood, set aflame almost as soon as he stepped away. He stumbled towards the stairs, and was nearly crushed several times by falling debris, but he made it there nonetheless. He stopped to rest up against the wall for a second.  Suddenly, a branch fell, but was caught part way down by a group of leaves.  It caught on one side, making it act like a pendulum, and it hit the Doctor in the back of the  head, knocking him out and sending him tumbling down the stairs.

The Master hovered in the air, still destroying Ponyville and murdering innocent ponies. He knew what he was doing would eventually drive the Doctor to face him, and when that time came, he would kill him. He fired one last shot at Sugarcube Corner, smiling when he saw a pink mare run out, her mane aflame.

It was starting to get dark out, the flames of the town glowed magnificently in the dusk light.  They reached and leapt several metres off the buildings, setting others around them on fire. He thought it was beautiful. All of this destruction, the death, and the pain, all of his own doing. The flames reached past Ponyville.  Starting without the grass fields that surrounded the town, the fire made its way outward, to the Everfree Forest on fire as well, and, if nopony put it out, it would most likely reach the neighboring towns.

“Now to finish the Doctor off...”

He flew over to the burning Library, which was just about ready to collapse. If the Doctor and his friends did not make it out soon, they would all die. “Hm.“  He grunted, ”Guess I’m going in.”

When the Doctor woke, he was in the basement, in a small pool of blood. The fall down the stairs had most likely broken some, if not most, of his bones. His head was throbbing, and judging from his surroundings, the Library was ready to crumble in on itself, burying him, Twilight and Spike inside. “Twilight....” The Doctor managed to choke out as he propped himself up with his front forelegs. Using a wall for support, he eventually managed to stand up on all fours.

He lifted one of his hooves up to his eyes, and saw a faint glow through the smoke.

“What? What!?  How... Am I regenerating? This universe is already destroying my Time Lord genetics... I’ll be lucky if the regeneration is able to be completed...” He put his hoof down and shuffled toward the bed they had put Spike in. He found Twilight beside the bed, cowering behind some debris, protecting herself and Spike in a shield of magic.

Chapter 10

“Okay, Doctor... Where are you?” The Master said as he bashed open the Library door and entered the burning tree. He looked around, trying to judge where he should go, and what place would be best to duck for cover if the Library fell in on itself. He decided to try the left and go down the stairs, but chose not to fly. If he did, his wings would more than likely be burnt.

He ran past patches of fire and ducked under debris as he made his way to the stairs. He jumped over a fallen branch, and made it to top of the stairs. “Now then...”

The Doctor grabbed Twilight and Spike, and put them both on his back. Strangely, he hadn't regenerated, but instead, the glow had healed him. Mending his bones and currently fighting the damage from the smoke. His legs were still weak, but he could carry his friends to safety if he ignored the burning pain throughout his body. “Argh! Come on, Twilight... and I've gotta make sure Spike doesn't fall off...” He took his first few steps, and nearly fell over, but he kept going. His friends needed him.

He slowly made his way to the bottom of the stairs, as a loud moan echoed through the Library. It was ready to fall. “I’ve got to hurry...!” He encouraged himself to move forward. As he slowly climbed the stairs, he made sure to not let Spike or Twilight fall. Twilight had fainted sometime before the Doctor had found her.

“Well, well well... Hello, Doctor...”

The Doctor looked up to see a grey Pegasus standing above him. “What? Who are you- Oh, no...”

“Yes. You know me.”

“Master...”

“Yes, Doctor... And now, I will be the one to finish you... Forever.”

Derpy had not listened to the Master. She had wandered through the bunker for hours, exploring. If the Master was really going to kill her, she knew, without a doubt, that the Doctor would save her before the Master got a chance. And that there was no way for the Master to harm her if he was not here.

During her exploration, she had found various rooms that held different things. She found fossils, plants, fossils of plants. She even found weapons, but they looked damaged and worn from age so she left them where they were. One room contained various works of visual art. There were sculptures, paintings, drawings and photographs. Many of the paintings were of famous ponies, such as Star-Swirl the Bearded, Celestia and Luna themselves. Yet curiously, there was also a painting for Princess Cadence and Prince Shining Armor, and nothing in the room had dust on it.

“If this place had been abandoned over 800 years ago... How are they here?” Derpy asked herself.

She startled when she heard a grunt come from behind her, and when she turned to look at the door she saw a Pegasus pushing the door open. He was carrying a large painting balanced on his back, using his wings to hold it still, and failed to notice the stunned Derpy as he entered the room. He set down the painting and looked at it for a moment before stopping. He turned around and saw the grey Pegasus staring at him.

“Well hello there.”

The Doctor adjusted his posture, and prevented Twilight or Spike from falling off his back.

“You caused all this.” He growled.

The Master chuckled. “Why yes, yes I did.”

“You murdered countless ponies! Innocent ponies! *Cough*... And you expect to get away with it?”

“Oh, Doctor... Always missing the obvious. I did all of this to lure you out. But, you seem to not want to cooperate... So I’m just going to have to drag you out and kill you myself.”

“But why? What do you gain from this?!”

“Nothing. It’s just fun.”

With that, the Master lifted his Laser Screwdriver with his hoof, and pointed it at the Doctor.

“Any last words?”

“Just two.”

“And what would they be?”

“Sonic. Screwdriver.” The Doctor pulled out his own Screwdriver, and pointed it at a branch. He activated his screwdriver and caused the branch to snap off, landing in between the two Time Lords. The Doctor took the opportunity to take cover.

“Ah! Doctor! Get back here!!” The Master roared as he flew over the barrier and rushed after the Doctor.

But the Doctor was quick on his feet, and made it back down towards the basement.

“Now... There’s got to be a window, or another staircase...” He said as he frantically looked around the room. “Nothing... Oi....” The Doctor turned around to see the Master fly down the stairs and land in front of him.

“Kill me if you like, Master. Just leave my friends alone.”

“Now, why would I do that, Doctor?”

“Because if you don’t-”

“What would you do? Come back from the dead and kill me?”

“Yes, I would!”

“You would kill me?”

The Doctor hesitated, then took a step back. “Let me pass.”

The Master flew up, and grabbed the Doctor by his tie as he struggled to keep Twilight and Spike on his back. “If I let you pass, you’ll run. You’ll run back into your TARDIS and escape into it’s endless rooms. It’ll be a never-ending game of cat and mouse.”

“If it means protecting my friends-”

“And you failed that, too!” The Master shouted, throwing the Doctor to the ground. As the Doctor hit the ground, he moved so that his passengers were not harmed. “You left her, Doctor. You left Derpy. I took her, and I’ll kill her.”

“Ditzy...”

“Is the little Doctor worried about his friend?" the Master teased. "Admit it, Doctor, no matter how hard you try, every time you run, someone gets hurt. And all the time, it’s the ones you love.”

“I-if you lay a hoof on her...”

“Look at you! Using pony language!” The Master shot at the Doctor with his Laser Screwdriver, but missed, and opened up a hole in the wall. It opened to dirt, yes, but if the Doctor could get him to aim at that spot again...

The Doctor moved in front the hole again, carefully balancing the bodies on his back, and stuck his tongue out at the Master.

“Can’t touch me!”

The Master fired again, but the Doctor stepped out of the way. The impact of the laser created a small hole to the surface of Ponyville to be revealed.

The Doctor smiled. "Well," he began, "we'll be off, Master. I've got friends to tend to."

The Doctor jumped through the hole, careful to keep his friends on his back. He climbed out and into the remains of Ponyville, leaving the Master to be buried in the collapsing library.

"The Master's not dead... He's survived worse... Why am I talking to myself?" The Doctor questioned himself as he turned to view the wreckage of the library. "Ow. He may not be dead, but he's gonna have a hell of a time sleeping that off."

The Doctor turned his head to his back as best he could. Twilight and Spike were still on his back. "Good... Let's get you two into the TARDIS..." He walked over to the blue machine, pushed the door open, and sighed. Still dead. The TARDIS was dead and nothing could change that.

He laid his two friends near the controls in the console room. He walked outside again and closed the TARDIS behind him. The remains of Ponyville weren't as bad as he expected, but they were still pretty bad. Ponies were buried under rubble, and several others lay dead on the ground, though most who were alive had fled. Some buildings were still burning and illuminated the town so the Doctor could see.

The Doctor growled. He didn't want to have to kill the Master, but if it came down to it he would.

A pony walked up to the Doctor. It was Colgate, the pony from before. "You have to help!" She said. Tears were slowly inching their way out of her eyes. "Ponies are dead! We need to get them out of the way!"

"Relax, Colgate." The Doctor then put a hoof up to his mouth, and made a "Shhhh...." Sound, and Colgate quieted down. "Now, then, dead ponies? We should go move their bodies."

Colgate looked at the Doctor with a look of confusion. "How did you do that?" She asked. "You- you just raised a hoof and-"

The Doctor repeated his previous action. "Shhhh...."

Colgate looked to the Doctor yet again, but didn't say anything.

"Let's go move a few ponies, but I will have to go soon."

Captain Jack Harkness

Colgate lead the Doctor a short distance from the library, where he saw charred ponies, dead or badly injured. “The Master will pay for this...” The Doctor growled. He looked to Colgate.

“Why’re you looking at me like that?”

“N-no reason... It’s just that... you seem so familiar...”

“What? How?”

Colgate’s eyes narrowed. “They way you walk... Talk.... the bowtie....”

“Yes, bowties are cool, but what do you mean I seem familiar? You can’t have seen me around, I’m not from here!”

“Who was that pony? The one who tried to kill me?”

“Him? He’s the Master. An old friend.”

“But- he looks so much like you...”

The Doctor shook his head. “There is no time for this. We’ve got ponies to help.”

He walked ahead of Colgate, and ended up in front of the burned remains of Sugar Cube Corner. Laying in front of the building were two fully grown ponies, and mare and a stallion.

“The Master committed genocide today. He will pay, I swear it.” The Doctor said, seemingly talking to the charred bodies. “Colgate, look around for survivors. I’ll start identifying the bodies.”

The Doctor walked away from the Cakes, and walked over to a bundle of ponies who had been shot through their torsos. “Raindrops... Cheerilee... Fancy Pants? What was he doing here? And.... Who’s this then?” The stallion, who was only chipped by whatever- presumably the Master’s laser screwdriver- hit him. This stallion had a deep blue coat with an even darker blue mane. He was wearing a jacket, one that the Doctor had never seen in Equestria before. His cutie mark was a constellation of stars.

“Did... Did you know him?” Colgate asked as she walked up to the Doctor. He had his head hung.

“I could have prevented this... All of it.... Had I just stayed away from my TARDIS after the Weeping Angels were done for, none of this would be happening...”

“What are you talking about? TARDIS? Weeping Angels? You do realize I’ve never met you before today.”

The Doctor turn around on the spot, looking at what remained of the town. Most of the fires had burned themselves out and there was no moon out tonight to illuminate what little was still standing.

See what happens. Everywhere you go, no matter how hard you try to save people, death always awaits them. Why don't you jus-

"GASP! Cough! Cough!"

The Doctor turned back to the dead ponies he was standing next to, to see the blue pony struggling to stand up as bodies slid off him.

"What?"

“What? How did I get here- Where’re my hands?!  Gwen? Is this some kind of prank?!”

The Doctor looked at the blue pony as he slowly got up, and looked around.  His eyes soon settled on the Doctor.

“Hello, there. I’m Captain Jack Harkness.” Jack said, with a sly grin etched upon his face.

Derpy looked at the new pony in confusion. So there was somepony else who had access to this bunker.... and could get out.

“Hello, there.” The Pony said.

Derpy’s face was a mix of happiness and confusion. Over noted by seeing another pony, but has no idea how this could be possible. “H-hello... What are you doing here?”

“I could be asking you the same thing.”

“I was kinda... brought down here by a... an acquaintance.”

“Well... I come down here with various artwork from all over Equestria,  decorate and maintain the place and have turned it into my personal collection. It has become a bit of a hobby and takes up much of the time I am not working.”

“Oh? So, you’re the reason there’s a painting of Shining Armor and Princess Cadence, even though this bunker’s been abandoned for centuries?”

“Yes, but I guess you could say that it is not abandoned any more. I stumbled upon this place one day when I was do field research. I decided to go deeper into the Everfree than anypony has been before, and ended up here. Though it's intriguing that not even the Canterlot Archives have any information on this place.

"But enough about that, we haven't properly introduced. What's your name then, Miss?"

“I’m Ditzy Doo, though... Some call me Derpy.”

“Derpy? Well, that’s not a very nice name.”

“I don’t mind it. In fact, my best friend calls me Derpy, but he doesn’t mean it like what other ponies do. He’s a nice stallion.”

“Well it is my pleasure Derpy, I am Sky Dancer.”

"Nice to meet you Sky Dancer.”

“Jack?!”

“Yeah, that’s my name. And, who, is that?” Jack looked behind the Doctor, directly at Colgate and grinned.

“Th-that’s my friend, Colgate.”

“Colgate, eh? Where I’m from, that’s the name of a toothpaste.”

Colgate took a step forward. “I’m a dentist, that’s probably why. And, might I ask, who are you?!”

“I’ve already said. I’m Captain Jack Harkness."

"Jack Harkness. You haven't changed a bit! Well.... Aside from the whole pony bit, but I'm going through the same thing..."

"Who are you? Have we met?"

"Take a good look, Jack. For some reason, this universe based the pony body off my previous form back home.... My Tenth, to be precise."

"Doctor..."

"'Ello, Jack."

"So, Ditzy, how long have you been here?" Sky Dancer asked the grey pegasus, who sighed and layed on her side on the couch, taking a bite out of the muffin she had made from the forge.

"I don't know. I haven't even seen the sunlight in days... Possibly weeks, or even a month! The Master has some kind of plan for me... I overheard him talking about that one night. He's crazy talking to himself."

"Hold on... The Master? What, do you two have some kind of role play relationship?"

"What? No! He.... Kidnapped me, one day after my friends and I came back to Ponyville."

"He kidnapped you?! What, why?!"

"I don't really know... But I am sure that my friends will show up and save me."

A silence fell between the two. Derpy looked at her muffin with sadness. Sky Dancer placed a hoof on her shoulder and looked at her.

"I'm your friend, right?" Sky Dancer asked.

She sat up and look back."Yeah..."

"And, I know the way out."

She began to smile. "You don't mean-"

Sky Dancer smiled back. "Yes I do. Ditzy Doo, you're breaking outta here."

Welcome Back

The Master slowly became aware of his surroundings. He was still in the library, as he was sure he hadn't moved. He was also in pain. The library must have collapsed, with him still inside. He had no feeling in his right foreleg, so he assumed it was broken. He opened his eyes to see nothing but dying fire and pieces of wood.

He laughed.

The Doctor had bested him again.

But, he would not give up. No, he would try again, and this time, he won't hesitate to kill the Doctor.

"Yes you will. You know that as long as I'm here, I'm not gonna let you kill him."

"Quiet, Doctor."

The Master strained to move his arm towards his Laser Screwdriver, and grab it. "Now, if you'll excuse me..." He fired the laser at the nearest thing he saw, and the resulting explosion knocked some more debris onto himself.

He heard laughing in his head.

"Shut up, Doctor!"

The Doctor stared at Jack, who did the same. "Doctor...."

"'Ello, Jack."

Colgate stepped beside the Doctor, and looked at him with a confused expression. "Doctor, who In the name if Celestia is this stallion?!"

The Doctor smiled. "Colgate, meet Captain Jack Harkness, leader of Torchwood Three. He's from my universe." The Doctor walked towards Jack and scanned him with his Screwdriver. "And has been here for a few hours. Strange.... Usually whenever he dies, he gets revived a few seconds... In fact... I would say he was one of the first ponies dead..."

Jack let out a small worried chuckle. "So, what? I can actually die now?"

The Doctor stayed silent.

"Oh...."

"Just be careful, Jack. Now, both of you, follow me. I'm pretty sure Twilight's awake by now."

"Twilight?" Jack asked curiously.

"Yes, Twilight Sparkle, Unicorn, Ponyville Librarian and student of Princess Celestia.

"But, she's in the TARDIS; we've better go get her. Come along, friends!"

When Twilight awoke, she kept her eyes closed. She could feel something soft underneath her and thought it was her bed. She laid there for a moment and hoped that the last few days had simply been a bad dream. That she was waking up on her soft bed, and all was well.

She slowly opened her eyes only to have her hope dashed away when she saw the TARDIS's console. She tried to sit up to look around, but was stopped by an incredible pain that swept through her body whenever she moved.

From her restricted, laying position, Twilight could see a magenta glow and realized what that was. When she saw Spike, it only confirmed that what she had been through had not been a dream.

She wanted to just lay there and weep silently; hoping that it would go away and everything would fix itself. But she decided that it wouldn't be the right thing to do right now. Spike was dead, yes, and she was hurt beyond recognition. But she had to be strong, and make The Master pay.

She slowly rolled off the couch trying to stand, much to her body's agony. When her hooves touched the cold metal of the TARDIS, a shiver coursed through her spine. She took a quivering breath, and lit up the dark room with a spark of her horn. She slowly looked around, and limped towards the door, willing it open with her magic.

"Oh? The door's opening. Twilight must be awake." The Doctor’s voice should have soothed Twilight but only made her feel worse. Had they stopped the Master? Is the Library okay? What happened to Ponyville? Would they now be able to save Spike? These questions and more rushed through her mind. Twilight backed away from the door as the Doctor pulled it open and stepped in. “Now, Jack, the TARDIS looks... a lot different from when you last saw it. When I regenerated, it kinda... blew up the TARDIS...”

Jack? Who’s Jack?

“And... Colgate.... Prepare for one hell of a ride.” At these words, Twilight's horn stopped glowing and she backed away from the door. She hobbled back to the couch and struggled to climb back on. Once she finally did, she tried to pretend she was asleep, but her erratic breathing prevented that.

"Welcome, my friends," The Doctor began. "To my TARDIS."

The doors creaked open even more, and hoof steps echoed throughout the dead machine. Twilight covered herself with the blanket. Something was wrong.

She heard a gasp come from the door. Colgate had just entered the TARDIS for the first time. She went back out the door and circled the TARDIS. Simply staring at it with eyes wide.

"Impossible!"

After running around it several times, and tapping on it repeatedly, she stepped back into the TARDIS.

"It's....! It's.... Bigger.... On the inside?!?"

The Doctor laughed. "Never gets old! I swear! Ah ha.... Anyway! Twilight? You up yet? The door was open..."

The Doctor stepped into the TARDIS even further, past a still bewildered Colgate as she turned back to circle the TARDIS again. "She's probably on the couch. Have a look around, Jack. It's home, for now."

The Doctor walked over to the controls. "It's dead, though. The Master did something to it when his new body formed... But what he did exactly, I have no idea." The Doctor sighed.

"You failed again, Doctor."

"No. Not right now..."

A burning yet cold sensation developed in the Doctor's hind legs, and progressively inched its way up his back, eventually filling his entire body. "I'm... Not... Like.... You..."

"Aren't you? You murdered the Time Lords. Lead the assault on Demon's Run, and killed countless, innocent, people. How aren't we similar?"

"I don't get.... *Ack!* A sick kick out of it..."

"Don't you? The Doctor, The Oncoming Storm. Just face it. You live the feeling of power when a life hangs in your control. You love it when you make someone pay for their sins."

The pain dissapeared just as quick as it came. The Doctor stumbled away from the controls, and a different voice rang through his head.

I've seen you in great dispare, Doctor. I've seen you in happiness and love. Pain and regret...

The voice seemed familiar, like an old friend.

Then it hit him.

The TARDIS was alive in his head.

"Welcome back, Sexy."

Moving Forward

A noise.

A noise that he hadn't heard for hundreds of years.

Thump. Thump. Thump. Thump.

He was finally free of the wreckage of the Library, a few scrapes and bruises littered his dark grey coat, but they didn't matter. What mattered now was getting back to the bunker.

Police and civilians crowded the remains of the small town. What had been a peaceful place for ponies of all kind to gather and socialize, was now reduced to rubble and charred wood.

And it was all his fault.

And he.... Was... proud.

He let out a small chuckle, gathering the suspicious looks of a few ponies. He simply smirked, and took to the skies, dust flying up from where he stood moments ago. "You're insane... You murdered innocent ponies!"

"Forget it, Doctor. You've committed your fair share of murder in your time."

I'm not the Doctor. I'm just his voice. Like how he hears you, you hear him."

"But why? Even I have no idea why that happened."

"When your current body was born, a little bit of your brain was transferred into his. Likewise, the same thing happened to you."

The Master didn't respond. He simply flapped wings harder until he was above the Everfree forest, it's trees running off into the horizon. Their green leaves turned a brighter shade, thanks to the rising sun of Equestria. "... How do I get rid of you?" The Master asked.

"It's simple. You kill the Doctor, but he has to kill you, as well."

"What?! Why?!"

"Neither of your minds are complete. He hears your voice in his head, tormenting him into madness. I am simply trying to complete myself once more. Once the Doctor is dead, your mind will be complete again, but, will be overwhelmed by having the brilliant mind of the Doctor, and your cunning mind, all in one brain."

"Like that Donna Noble..."

The voice in the Master's head stopped. A sound, as if it were breathing tormented his ears.

"Don't mention her."

"Did I strike a chord? If you don't want me to mention her, then tell me this: is there a way to make me complete, and live?"

The voice of the Doctor didn't respond.

"Rubbish, you are. Rubbish!" The Master descended into the forest, where he landed without a sound. He looked around, and walked over to a patch of grass. Shuffling around in it, he eventually hit his hoof on something metal. He lifted it up, revealing a stairway, leading into darkness. He took a look over his shoulder, and hopped in.

The Doctor laughed.

“Y-you’re alive! In my head! Oh, my god, this is the best news I’ve ever had!”

Doctor, you really must get a hold of yourself.

“*Ahem.* Oh. Yes. Sorry. But- how did you- did the Master- What is going on?!”

A tear. A tear in the Rift has opened.

“That’s how Jack got here...”

Exactly. Now, if that rift happened to tear at that exact moment a being was born, through a being who has had more contact with the void than any living being, it would have some interesting side-effects.

“That’s why the Master is getting stronger.”

“Doctor?” Jack called. “Who are you talking to?”

“N-no one, Jack!” The Doctor stuttered. he turned to Jack. “H-have you gotten a better grasp of what the TARDIS is like now?”

“I gotta admit, I like the Coral desktop theme better.”

The Doctor beamed. “Down that hall,” He pointed his hoof to the south of the console. “Take two rights then a left. The TARDIS saves any, and all themes I’ve ever had and will have."

Jack nods, and begins his walk.

"The Master... He needs to be stopped.... Twilight? Are you awake?"

Twilight slowly got up, and walked over to the Doctor. "How.... How long have I been out?"

"About an hour or two. I have somepony I would like you to meet, once he gets back. Colgate? How're you holding up?"

The dentist looked to the Doctor with a smile on her face. "Doing great. Still a little freaked out, but I'm ready to take down this Master guy. He ruined Ponyville, who knows what he'll do next?"

"You're right, Colgate. Which is why we need to alert the Princesses about him. He's insane, and has mild control over the Void, the space between dimensions."

Colgate and Twilight were shocked.

"If he really is as insane as I predict... He'll likely risk killing himself to get to me. If he does rip a hole into the Void, then not only will we be fighting for ourselves, but for the entire planet."

Despite his best efforts, a smile etched its way onto the Doctor's face. "All of Ponykind rests in our hooves..."

He looked to the two of his companions.

"We've got to alert the Princesses, then we find Derpy." The Doctor runs toward the console, and flips a switch, but nothing happens. His face turned pale. "R-right.... TARDIS is dead..." He laughed a little, his face turned a shade of red. “Ahem... Looks like we’re hoofing it. Jack, you’re a Pegasus... You could fly, if you knew how to. And Colgate, you and Twilight are unicorns... You two could teleport us to Canterlot.”

The Doctor closed his eyes and sighed. “It’s my fault this is happening... If I had finished the Master where he stood in the Library, none of this would be happening... We could find Derpy, we could bring Spike back to life, but we can’t, because I was a coward!” He brought his hoof down on the metal floor, causing a clang to echo throughout the dead TARDIS.

“Doctor,” Colgate began. “calm down. We’ll beat this guy.”

The Doctor’s head shot towards her. “How do you know that?! You saw what he did in Ponyville! And that’s not even all he’s capable of! He can take over entire planets within a day! You haven’t faced him before. He’s one of the most deadly enemies I know. He is a monster.”

The Doctor hung his head. “If you plan on helping me, you must know one thing. You will, more than likely, die. You see Spike, floating in the ball over there?” He pointed his hoof towards the magenta sphere encasing the dead dragon. “He did nothing. All he was doing, was watching the console. He was murdered in cold blood!”

He sighed. “The Princesses. Twilight, could you teleport us? I’m sure the Princess still remembers me. But from where?” The Doctor’s face turned from one of sadness to one of confusion.

“Uh...” Twilight stuttered, still recovering from the Doctor’s outburst. “Sure. Where’s Jack?”

“Oh! He should still be in the old console room.” The Doctor ran towards a hallway on the back wall of the console room.

“Jack?” He called. “We’re about to leave!”

A few minutes later, the Doctor and his companions were gathered outside of the TARDIS. Twilight stood in the center of the circle they formed, her horn glowing. “Okay... When we land, you may feel lightheaded. Just a warning.”

“Sounds just like a Vortex Manipulator,” Jack laughed.

The Doctor gave a small chuckle. "Okay, Twilight. Let's go."

Twilight nodded. Her horn started to glow even more, nearly blinding her friends.

The Doctor looked around. His friends were all there, prepared to fight.

"I have a tendency to pick up fighters, don't I?"

The Master stood in the center of the main room of the bunker. Where was Derpy? She couldn't have had escaped. Taking another look around, he noticed that a door to the far right as left ajar.

"She's gone exploring." He noted. He walked over to the door, and pushed it open further.

"She'll escape, eventually."

"Not if I have anything to say about it."

"You're not in the position to say anything. You're not well, Master."

"Not well? Ha! I feel better than ever!"

"The sound of drums. You're hearing them again."

"And?"

"The signal. It's coming from somewhere. It's driving you insane, faster than last time."

“The signal? How do you know it’s a signal?”

“I don’t. I could be wrong.... But from last time this happened, it didn’t really end well for either you or the Doctor.”

“Bah. Just shut up already.”

The Master tuned out the voice in his head. Derpy still needed to be found. He turned a corner, which led into a hallway with several doors.

Derpy and Sky Dancer stood in silence. Sky had been shocked at the revelation that she had been kidnapped by this “Master” character, like anypony would have, but she just sat here, and waited for her friends to save her. Well, that seemed kind of foolish, if you knew somepony who knew the way out of the place you’re being held at.

“You’re going to break me out of here?”

“Yes, I am. You’re being held here against your will. I know the way out of this place. I’m getting you out of here.”

“But what if the Master sees us?”

“He won’t. I promise.” Sky looked behind himself towards the door, making sure the Master wasn't there. “We just have to make sure he doesn't. He’s not here, is he?”

Derpy thought for a few seconds. “No. He left a while ago.”

“Then we don't have much time. If he has been gone that long, he could come back at any moment.”

Sky took her hoof, and ran towards the door, pushed it open, and ran down the hall.

“The exit is this way. If he’s coming here, then we've got to be fast!”

Captain Jack Harness

POP!

The Doctor felt grass under his hooves once more, a feeling he missed for the whole five seconds it was gone, and stumbled over himself and fell as his eyes refocused on the landscape. A garden. His head swimming, he reached a hoof out and found one of his companions. “T-Twilight? Is this you?”

“Why, Doctor, I didn’t know you swung that way.”

The Doctor’s vision immediately refocused, and he found his hoof lying very low on Jack’s stomach. “G-gah!” The Doctor withdrew his hoof right away, and stood. “Y-yes, uh.... Is it hot out here?”

Jack let out a short chuckle. “Ah, Doc, I’m never gonna get used to this new you.” Jack got up and walked past the Doctor, tapping the Time Lord with his tail as he did so, causing the Doctor’s face to flush. “C’mon, Twilight and Colgate are over here.”

“Ah- yes- um.... Right....” The Doctor turned to see his other two companions being helped up by Jack. “Twilight, we seem to be off by a few miles.... We’re right outside the Castle Labyrinth...”

Twilight shook as she fought to stand upright. “Ooh....My head..... What was that Doctor....?” Her voice trailed off as she realized where they ended up. “My spell was off....”

“Yes. Yes it was. No matter. As long as nothing else went wrong, we’re fine.” The Doctor whipped out his Sonic Screwdriver and scanned the area. “Yup. 2012. Or 1002, in your time. We’re in the right dimension, as it would seem.... Nothing wrong here.” The Doctor grinned at the Labyrinth before them. “If I’m correct, this is where Discord wrecked some chaos earlier this year, am I correct?”

Twilight trotted up to the Doctor, her balance fully regained. “Yes, that’s right. How did you know that?”

“Oh, I’ve been around for a while, Twi’. Even before you and your friends discovered who I am, I’ve been here, silently assisting you. The return of Nightmare Moon, Discord, hell, even things that haven’t happened yet.” Another grin crossed his face.

“What kind of things?”

“Spoilers.” The Doctor jumped and clopped his hooves together, landing back down with grace. “Anyway! Princesses! Warning! Jack, why are you kissing Colgate?!” The Doctor finished as he turned towards the dark blue Pegasus and the blue Unicorn. “Th-this is NOT the time for this!”

The two broke apart, and Jack smiled slyly at the Doctor. “You know me, Doc. Can’t help myself.”

The Doctor grumbled. “I knew I was right about what you’d do here. Can’t leave you alone with a mare. Or stallion.” Jack grinned at the Doctor in the mention of stallions. “I-Including me, Jack! now, Colgate, get behind Twilight. Jack, you stay behind me.”

“Well, if you insist, Doc-”

“I-I DIDN’T MEAN IT LIKE THAT!” The Doctor’s face was white as a ghost at this point, though a tint of red could be seen on his cheeks. Jack chuckled again, following the Doctor as they walked past the Labyrinth and towards the castle. “Jack, behave, please. The world, no, the universe is at stake here!”

“Sorry, Doc. You know me.”

“Twilight, keep an eye on Colgate.”

“Yes, Doctor.”

“And Colgate, you behave yourself, too.”

“Yes, Doctor...”

“Now, everyone, please be good until we get to the castle, then, Jack, you and Colgate can kiss all you like while we stop the Master from whatever he’s doing!”

The Master laughed.

They thought they could get away. Derpy and that stallion. They thought that they had a chance.

They were wrong.

“You thought I wouldn’t think to not be gone for long? Do you take me for a fool? If anything, you’re the fool, my dear Derpy.”

Sky shuffled in his metal restraints that bound him to the wall, a look of anger crossing his face.

“What? Did I hurt your feelings? Do you not want me to insult your retard friend?”

Derpy gasped at the insult, but stood in place.

“If you were smart, you wouldn’t have wasted your time talking, and you would have been long free of my grasp. But no, you decided to be idiots and stay!” The Master stomped, and took a heavy breath. “I don’t know why I even bother anymore. The Doctor’s not coming for you. If he was, he would have already come here!”

“Y-you’re wrong! He’ll save us-”

“How can you be so sure?! Because he’s the Doctor?! He’s a hero?! I seem to remember one Doctor where he doesn’t give a damn! And that same damn one beat you within an inch of your life, simply because you annoyed him!”

Derpy looked at the Master. “N-no.... You’re-you’re lying!”

“Then there’s one that killed you! And another that left you to be putty in Discord’s hands!” The Master’s eyes grew red, and his smile turned to one of a madman. He dashed towards the grey Pegasus,  and stared her in the eyes. “The Doctor is not coming to save you. He doesn’t care. He will fall, this day. He will die. Your precious Doctor will die!”

“So, now, if you excuse me, I must be off.” The Master turned towards the door, and chuckled. “How would the Doctor say it? Allons-y! That’s right! Ha, ha ha!”

The Doctor and his friends reached the front of the castle, where they were stopped by two of the Royal Guards.

“Halt! Who are you?!” The chant in unison.

The Doctor hot out his Psychic Paper -which he was thankful he didn’t leave behind- and calmly lied.

“My name is Dr. John Smith. These are my associates. We were summoned by the Princesses.”

The First Guard looked skeptical. “The Princesses didn’t mention having any visitors today.” He said, glaring at the Doctor.

Jack chuckled. “If you don’t believe us, then go ask her yourself. We’ll be waiting out here.”

“Not so fast, pretty boy.” He glared at Jack now, and pointed to the other guard. “You watch these four. I’ll go talk to the Princess.” With that, he turned, and walked away. Jack grew a sly grin on his face, and stepped towards the other guard.

“Hello. I’m Captain Jack.... Harness. Captain Jack Harness.” He extended a hoof towards the guard, who grew an uneasy expression.

“I’m.... ah.... Golden Spear....” The guard stammered. As uncomfortable as he was, he extended his own hoof to meet Jacks, and they shook. “N-nice to meet you, Mr. Harness. What relations do you four have with the Princesses?”

“We’re.... Well, John is an old friend. Aren’t you, John?”

The Doctor smiles. “Yes, well... Jack, can I talk to you and Colgate?”

“Uh.... Sure, John....”

“Yes. Right.”

The three walked a ways away from the guard. “Alright.” The Doctor began. “I’m going to be honest with you. I have no idea how the Princesses know me.” The statement brought two raised eyebrows from his friends.

“Doc, how can you have no idea how The Celestial Sisters know you?”

“Yeah, that seems like a heck of a thing to forget.”

The Doctor gave a nervous laugh, and rubbed the back of his head. “Back before all this began, Derpy, Twilight and I stopped these things called The Weeping Angels, from invading Equestria. They got to the castle.... But we caused a time paradox and they all died.”

Jack raised another eyebrow. “What.... What was the paradox?”

The Doctor gulped. “Uh.... Derpy. The Weeping Angels sent her back in time, and she died in the future. For us, it hadn’t happened yet, so she jumped off the top of the castle in order to prevent that. This caused a paradox, and the Angels died.”

Jack shifted his weight. But... The fact that she died.... is just that. A fact. You can’t just.... Get rid of a fixed point.....

The Doctor, however, didn’t notice Jack’s confused face, and kept explaining his previous adventures to his companions. “And then, after we woke up next to the TARDIS, Twilight decided to bring Spike along.... And well, here we are.”

“Ah.. Doc?”

“Hm? Yes, Jack?”

“You do realize that... Derpy’s ‘death’ was a fixed point.”

“And we stopped it.”

“That.... What? You can’t get rid of a fixed point.”

The Doctor waved a hoof at him, and walked back towards the castle. “Don’t worry, Jack, if there were any consequences, we would have seen them by now. Last time a fixed point was removed, all of history started happening, all at once!” The Doctor let out a chuckle at the memory. “Besides, even if it wasn’t a fixed point, there wouldn’t be any reason to fret. There’s no reason to worry.”

The other guard returned back at his post, and let out a small sigh as the Doctor and friends walked back to the gaurds. “Princess Celestia has testified that you are welcome inside the castle. You may enter.”

“My friends, too?” The Doctor asked.

“Yes. You and your friends.”

With a smile, he, Jack, Twilight and Colgate walked past the two guards, and into the castle.

As they walked past, Golden Shield glanced at Jack, who didn’t notice. Golden Shield turned to his friend, and whispered “Do we have any records of a ‘Captain Jack Harness’?”

Beginning of the End

"My Princesses!" a Guard exclaimed, bursting through the doors to the throne room. "You have urgent visitors!"

Celestia raised a brow. Visitors? The Day Court was over, and the Night Court would not begin for over two hours. "Who are these visitors?"

The Guard straightened his posture, finally catching his breath. "The brown one calls himself 'Doctor John Smith'. Others named Jack Harness, the dentist Colgate and your student Twilight Sparkle are here as well."

At the mention of Twilight, Celestia's smiled. "Ah, my student. Though it is nice to see her again... Her company perplexes me..." Of course, she knew all too well who they were. Her Doctor was here again. "The only other one I recognize is Colgate."

Luna's smile, however, faded. How much longer must We keep this charade, dear Sister? Surely the Doctor's time stream has caught up...

Just a little longer, LuLu. The Doctor will know everything all too soon. "Send them in. My sister and I would like to see them at once."

"Yes, Princess!"

A few minutes passed, and eventually Celestia saw the ponies she was waiting for.

Her Doctor was finally here.

"Doctor John Smith, at your service, My Princesses." The Doctor bowed, and his companions did the same.

"No need, Doctor. Rise, my friend."

The Doctor froze. "That's... Something I would like to talk to you about, Celestia."

See, 'Tia, he is not yet aware.

.... I see that, Sister.

"The first time I met you was when I first entered Equestria from my universe. I was taken here on request from my companion, Ditzy Doo."

Not from my perspective...

"And since then, we've only had one short meeting. And that was erased from time."

"With the Weeping Angels."

"Precisely. So, there's no way you can know me enough to trust me with waltzing in here unannounced. Who are you, Celestia?"

Twilight poked the Doctor in the ribs, pretending to cough. "Doctor! The Master!"

"Quite right. Sorry, Twilight." The Doctor's gaze hardened. "As I'm sure you're aware, there was an attack on Ponyville yesterday."

"Yes, Princess Luna and I were informed mere hours after it began."

"The pony who attacked the town was another Time Lord, like myself. The Master."

'Tia. This 'Master' was seen fleeing the town into the Everfree Forest. Towards the-

That place is long gone, Luna.

But not forgotten.

"He was brought into Equestria by a number of factors. The paradox we caused to stop the Angels, and the TARDIS's connection to my universe. It pulled his soul here from the afterlife.

"His soul then found a way to tap into my dark side. The side that holds my evil, and my darkest secrets. He is the Master, but at the same time, he is me."

The Doctor jerked, as if he were in pain, and rubbed his head, mumbling as if he were talking to someone.

"Ah... We... Something backfired with his revival, though. A piece of my mind went with him, and his with me. His voice torments me, and I assume mine talks to him."

"And why have you come here, Doctor?" Luna questioned. She was happy that the Doctor was here, but why tell her when he has stopped worse?

"The Master is one of my toughest foes. The last time I faced him in my world, I died. And this time, he wants to make sure I stay dead. And he'll kill anyone who gets in his way. He's already killed Spike, and countless others."

Celestia turned her head to Luna. "Sister? Your thoughts?"

Luna nodded, and put on a fake face of distrust. "What you have said, Doctor, We don't exactly believe it."

"I didn't think you would. But-" suddenly, the Doctor's nose flared, and he whipped around to his companions. "He's here." His face turned grim, and he whipped out his Sonic Screwdriver. “Derpy’s not with him. Her body signature’s still out of reach.

“Princesses, I need your help. Please, use your magic to place a barrier between this dimension and my own. The Master- I think he’s trying to rip a hole in the Universe, just to kill me.” The Doctor’s words changed in tone. They changed to ones of worry, and fear. Not like the Doctor that Celestia and Luna knew.

Celestia’s mouth grew into a slight smile. Oh, how she had missed this. “..... Doctor, I will help you.”

The Master laughed. His plan would finally come to fruition. After all this time, all the energy wasted on luring the Doctor out, and kidnapping that retard, it would finally happen.

You’re insane. The voice of the Doctor rang again.

“I thought I got rid of you.”

Not until the Doctor dies.

“So, you’re on my side, now?”

... No.

“No matter. My plan is almost done.”

Your ‘plan’ will get everypony killed.

“No. Just the Doctor. I’ll make sure of that.” The Master held his Laser Screwdriver is his hoof, and pointed it at the Princesses’ throne room. “I just need to lure him to me. And at long last, I will be victorious.”

He fired, and the laser struck its target, and the throne room erupted into a ball of flames.

“..... Doctor, I will help you.” No sooner than the words left her mouth, her throne erupted into a burning death trap, which would have killed her, had she been a regular pony. The explosion merely charred her fur. But her throne was the least of the damages.

She fell onto her side, and looked to her sister. “Luna! Get them out of here!”

Luna’s throne too exploded, along with the walls and floors. Chunks of ceiling fell, nearly crushing them, the Doctor and his friends. “We shall not leave thee, Celestia!” Luna’s horn ignited, and a rock that nearly crushed Colgate was blasted out of the air. “If We must leave, thou are coming, as well!” Another explosion, and the Guards stationed outside screamed.

The Doctor looked out of the space where the walls used to be, and looked down into the Gardens. “The Master. Jack, Watch Twilight and Colgate. I’m going down.”

Jack nearly fell over in surprise. “N-no, Doc.” He stepped over to the Time Lord’s side, and placed a hoof on his shoulder as another explosion erupted behind them. “If you’re going, we’re going, too.”

"J-Jack, I can't have you in danger. You know how ruthless the Master is."

"Which is exactly why we're going."

The Doctor sighed in defeat. "Fine. Princesses, I would appreciate it if you got to work on that shield. We have a Time Lord to stop." The Doctor flashed a grin, and straightened his bowtie. “Alright, lads... Geronimo.”

The End (1/2)

Sky Dancer and Derpy hung on the wall, all spread out for the world to see. Yet there was no one there to see them. They were suspended with chains by their fore legs. Though they had not been hanging for very long, it felt like an eternity. The Master had only been gone for a few minutes and Derpy had already started to try and shake free and escape.

“How are we going to get out of here?” Derpy asked as she struggled against her restraints.

Sky turned as much as his restraints allowed, so he could look to Derpy in the faint light coming from behind the door. “I am not sure, but we will figure out a way. For now, please let me think.”

Derpy nodded. And so they hung in the dimly lit room as Sky stared at the ceiling while he thought.

“Hey Derpy.”

She jumped at the sound of Sky’s voice, it had felt like an eternity since he last spoke. “Yes?”

“Can you get your wing out from behind your back?”

“Maybe,” she said as she struggled to do so. Derpy was able to get her wing from behind herself and extended it out in front of Sky.

“Good. Now, hold still.” He took one of her feathers in his mouth and pulled it out with a swift turn of his head.

“OW! What’d you do that for?”

“You will see.”

Sky then proceeded to adjust his position so that he could see the lock on his right hoof. He pushed himself away from the wall and spun so that he was now facing the wall so that the two chains holding him up were crossed. He then placed his two hind hooves against the wall and pushed himself into a partial standing position. Sky then forced the feather’s shaft into the lock mechanism and started to move it around.

Derpy gave Sky a puzzled look. “Are you trying what I think you are?”

“No, I am not try to pick a lock with a feather. I am trying to destroy the lock’s mechanism. All most... “

SNAP!

“There.”

Sky started to flap his wings and move away from the wall. He raised his right hoof and smashed it against the wall. The metal restraint fell open and off his hoof. He then proceeded to work on the other hoof and repeated the process which ended with the satisfying clatter of the metal against the cement wall.

“Alright, now we have to get you out.” Sky looked at the restraints on Derpy’s with puzzlement. “But I don’t want to accidentally hurt you if I do the same.”

“I don’t really mind.”

“But I do.”

Derpy nodded, and looked around the room for anything that could help them. The small room didn’t hold many items, only a few spaces for ponies to be hung by their hooves, a table and the door. “Is the door locked?” She asked.

Sky looked over his shoulder, turned and started walking towards it. “I do not know. Let’s see.” He tried turning the knob, and much to his surprise, the door swung open. “That... Was not expected.”

“The Master must have been in a hurry...”

“So are we. I’ll go check the other rooms. There has to be a key somewhere.”

“Jack, do you know how to fly?” The Doctor looked over his shoulder to look at the dark blue pegasus, who hurriedly shook his head ‘no’. The Doctor sighed. “I’m not risking Twilight teleporting us down. She’s already magically drained...” With a growl, the Time Lord stomped his hoof, and angrily glared through the gaping hole in the wall.

Then, a purple hoof rested itself upon the Doctor’s back.

“It’s okay, Doctor.” Twilight smiled. “I’ll be fine.”

“No.” The Doctor stated firmly. “I can’t- I won’t risk your wellbeing. Jack has a healing factor- he can come back to life, even, but you can’t. I am not risking you.” He sighed. “I’ve already lost Derpy...”

A familiar laugh echoed from below the trio, as the Princesses focused on getting everypony out of the castle.

“Is that everypony, sister?” Luna shouted over the commotion of panicked ponies.

Celestia nodded solemnly. “Except for the Doctor and his companions, yes.” She glanced back towards the ruined castle, fire and smoke swirling into the sky. “I need you to find them, and once you do we will apprehend the Master.” The white alicorn then glanced back down to the crowd of ponies, some of whom were Guards trying to calm with no avail.

“Understood. ‘Tia, We will see thee soon.” With that, Princess Luna flew back to the castle.

Pop!

The Doctor felt the stone of the pathway to the Royal Gardens beneath his hooves once again, and immediately fell to his knees. “T-Twilight!” He gasped. “D-Don’t do that anymore!” He said as he slowly straightened himself, and looked back worriedly at the purple unicorn, who gulped.

“D-Doctor...”

The brown stallion turned slowly, revealing his long time enemy. The one who currently took on a dark version of his current self.

“Hello, Doctor.”

“Master.” The Doctor’s head hung slightly, but not in worry. In anger. The anger of so many innocent lives lost. “You’re insane.”

The Master scoffed. “Oh, please, tell me something I haven’t heard from you, Doctor. ‘Now, Koschei, don’t destroy the universe!’ ‘Now, Master, don’t kill a third of the human race!’ It’s always, you, Doctor. The one who always defies me. What right do you have to order me? To treat me like I’m some kind of animal who needs taming?!” The Master fired his screwdriver directly at the Doctor who, along with Twilight, was able to scramble out of the way. Jack was not as lucky, and got hit directly in the chest. He was sent flying; a black scorch mark was emblazoned on his coat.

“Jack!” The Doctor and Twilight cried in unison.

The Doctor glared at the Master, who fired another blast from his screwdriver at the Doctor. The Doctor shoved Twilight out of the way and barely made it himself. “You destroyed Gallifrey! The planet we grew up on together! Played together!” Another blast missed the Doctor by more than a few inches, instead hitting a strangely familiar statue.

“You killed the Time Lords! It’s time for me to finish the job!”

The Doctor grabbed Twilight by the hoof, whispering a low “Run!” as the pair took off, dodging blasts from the Master.

“Get back here, Doctor!” The Master yelled as he stiffened his wings preparing to take off, but a voice stopped him.

“Stop there, fiend!” The voice of Princess Luna’s Royal Canterlot Voice echoed through the destroyed Gardens. The Princess of the Night landed a few steps behind the grey stallion, who showed no signs that he noticed her.

After a few seconds, he finally spoke. “I suppose you’re here to... Let me guess, kill me? Take me to your sister to face my crimes?”

“We hath no intention of taking thy life.” Luna spoke smoothly, showing no emotion. “We wish for thou to drop thy weapon.”

The Master chuckled slightly. “Oh, you mean this old thing?” He said, holding up the screwdriver. “I mean, I am more powerful than you, and it’s obviously going to be an unfair fight, so it would only be right of me to even the odds for-” He interrupted himself, firing the weapon directly at Luna who was unable to avoid the attack. The laser hit her square in the chest. She stood fast but only for a brief moment before she collapsed under her own weight.

The Master simply smiled. “And I thought you’d be a challenge.”

Celestia paused.

“I... apologize, my subjects...” She said, blinking away a tear. “I... must go.... I fear something has happened to my sister... Princess Cadence will be here shortly. She will take over as ruler for the time being.” With that, she flew into the air, speeding towards the castle.

“Please Luna,” she begged. “please be okay...”

The Master slowly walked along the pathway, his gaze drifting from statue to statue.

You said you wouldn’t kill anypony. The voice of the Doctor growled.

“I said that my plan shouldn’t get anybody killed. I never said it wouldn’t.” Another growl echoed in his head. “Oh, shush you. If you don’t want anybody else killed, then find some way to kill me so you can go back to being the ‘Doctor’.”

The Voice didn’t respond.

“D-Doctor! Jack was k-killed!” Twilight cried. “The Master killed him! We have to stop him!”

The Doctor stomped his hoof. “Relax, Twilight! Jack is fine.”

“H-how can you say that?! I saw it! His body flew-”

Just then, a blue hoof wrapped itself around Twilight’s waist. “Aw, you were worried about me,” the charming voice of Jack Harkness sang.

With a yelp, her hoof smacked Jack across the face, much to the amusement of the Doctor. “You- you were dead!” She yelled.

“Yes, yes I was. And now I am not. Now, quiet, or the Master will find us.”

“But...but how!?”

“Time mumbo jumbo. Even I don’t understand it. Now, hide!” Jack said, pulling Twilight aside behind a nearby statue of a Celestial Guard. The Doctor ran after them, but a familiar blast erupted past the Doctor, stopping him in his tracks.

“Not so fast, Doctor,” The Master growled, slowly walking towards the Doctor. “This ends here.”

Unstable Relationships (Written by Both Sonic Mario3 and Dartrunner)

“Derpy!!! Where are you?!” Twilight yells.  Her eyes red from the tears that roll down her face, she looked around the control room, searching for the grey Pegasus.  She set the Doctor down on the bench by the control panel and frantically moved to the entrance of the TARDIS.  She looked to see if Derpy was outside.

Seeing no sign of Derpy, Twilight retreated inside to find The Doctor laying, stretched out on the bench, trying to block out the voice in his head and the pain that filled his body.  Breathing heavily, he spoke, "Twilight... Derpy is most... likely alive.”

Doctor...

“We can find her... but first... we must attend to Spike. Go to the library... and find that spell.  I'll catch up...

She turned to look at him, thought how he always puts everyone had of him, then nodded.  She then proceeded to the entrance.  Spike was still of her back, he looked as if he was sleeping, something quite normal for him.

She turned toward the library as she exited the TARDIS, and started to walk.

As the Doctor willed himself to his hooves, he mumbled to mumbled self, "I could use a cup of tea."  He forced himself to limp toward the door, to follow Twilight.

Remember, Doctor... All those who have died in your name...

He stumbled down the ramp and fell through the door, stiffly hitting the ground.  He could see Twilight close to the library.  She turned her head to look at the TARDIS, when she saw that the Doctor was lying on the ground, she turned around to go help.

"No! Don't worry about me! Go help Spike!"  The Doctor could see Twilight hesitate.  "GO!!"

The Doctor saw Twilight turn back to the library before he blacked out, lying half inside the TARDIS.

Twilight started to walk toward the library with Spike on her back.  This looked fairly normal, Spike would often sleep on her back after a long day. The only hint at a problem, was that she was clearly grief stricken.  Yet no pony was around to notice.

As she neared the library, she turned to look at the TARDIS.  Panic filled her when she saw that the Doctor was lying on the ground.

The Doctor shouted, "No! Don't worry about me! Go  help Spike!!" Twilight hesitated.  She was conflicted between him and Spike.  "GO!!"

Twilight turned back to the library.  She opened the door, and sent Spike down inside.  Twilight looked around the room, at the shelves of books covering the walls.  Not sure where to look, she started removing books at random and flipped through them.  The only thing for sure she knew about the book was that it was about biology.

By the time she found the book, several minutes had past, and there was a moderate pile of books beside her.  Twilight held the book in front of herself with her magic. She read over the spell twice, then took a deep breath and concentrated.

“I.. can do it... I must do it...” A young man says. He had brown hair, pale skin and brown eyes. He was wearing ragged clothing, a pale yellow shirt that had brown sleeves, and brown pants. He was aboard a spaceship, and he was at the controls, trying to redirect the ship from hitting Planet Earth. He continues typing away at the controls.

Meanwhile, a Cyberman, holding his blaster, limps down a railing, which leads to the young man, whose name is Adric.

“Scott to TARDIS, Scott to TARDIS!” A voice says over a messaging intercom. A lady grabs the Walkie-Talkie, and speaks. “We have Cybermen on board! Repeat, Cybermen on- Ah!” The lady is cut off when an attacking Cybermen grabs the walkie-talkie out of her hands, and holds it as a man’s voice says over:

“I’ve escaped, but Adric is still on board!”

The Doctor’s face turns to shock. This Doctor was the Fifth, he had blonde hair, a jacket that had orange tips, and also bore a celery. His pants were the same color as his shirt and jacket. He fumbles Adric’s amulet in his hands, worrying for his companion.

“Adric is still-” Scott says, but the Cyberman crushes the Walkie-Talkie.

“You have failed, Cyberleader.” The Doctor says. The Cyberleader turns around, and if it had eyes, the Doctor was sure that they would be cutting into him lie razors. The Doctor keeps his hands behind his back as the Leader approaches him.

“BUT YOU WILL NOT ENJOY THE VICTORY. I WILL NOW KILL YOU, DOCTOR.” The Cyberleader says, slowly holding his gun to the Doctor, who turns Adric’s amulet in his hands behind his back.

Suddenly, Tegan jumps onto the Leader, followed by the Doctor, who breaks Adric’s amulet, and feeds the shards into the Leader’s chestplate. The Doctor jumps off of the Leader, and ducks behind the TARDIS console with Tegan, who screams as the Leader starts firing around the TARDIS, making gurgling sounds as he does so. The Doctor then grabs the gun from the Leader’s hands, and shoots him down.

Time Passes....

Adric continues working on the controls, when a Cyberman comes in, and shoots at Adric, who dodges, but the blast hits the controls. “N-no!” Adric says as the Cyberman falls over from a lack of power. He runs over to the controls, and finds that he can do nothing...

He swallows.

And the ship impacts the Earth.

The Doctor woke with a jump.  He wondered why he was lying in the dirt.  He looked toward the library, only to be reminded of what had happened.

In a frenzy he started toward the library, running as fast as he could in his weakened state.  When he reached the library he burst through the door and saw Twilight standing near the centre of the room with a book floating in front of her.  He stood panting as her horn came alight.  He collapsed onto the floor to rest and to try to recuperate.  The Doctor looked on as Twilight began to work.  He knew better than to interrupt a unicorn when one was performing magic, especially at this time.

Even unicorns who are masters at magic have difficulty concentrating when they are emotionally distraught.  One cannot focus fully when they are distracted.  But, at this point, unicorns are at their most powerful, driven by the emotion, and most unstable.

Master...

The Master awakes from his sleep. He looks around, searching for the voice, but finds nopony other than the sleeping form of Derpy Hooves, laying where she had woken up hours before. “Who’s there?” The Master asks, but no answer comes. He pulls out his Laser Screwdriver, which he had made from spare parts in a nearby dump, and points it into the darkness of Celestia’s bunker.

“Who’s. There?”

Master...

“Doctor? How did you find me?!”

Master...

“Come out, Doctor! Face me!”

You’re insane, Master. An abomination created by our race for war, yet you ran. How does that feel? It’s what I’ve been feeling my entire life.

“No... No! I’m not a coward! You, however, run and kill the people close to you!”

Derpy stirs.

“Wha.... Master, who are you talking to?”

“Did I tell you to talk?! Go back to bed!!”

Derpy lays back down.

“Listen, Doctor;” The Master spat the Doctor’s name. “I’m not sure what’s going on, but I do know this: I’ll make your life a living hell. Do you hear me?”

The Master then looked to Derpy, who was peacefully sleeping.  He let out a sigh. “After I get a good night’s sleep...”