Doctor Whooves 3: The End of the Universe

by Draconaquest

Rating: everyone
Tags: Princess Cadance, Comedy, Adventure, Shining Armor, Twilight Sparkle, Crossover, Doctor Whooves, Roseluck, Drama, My Little Pony: Friendship is Magic
Length: 8443

While in the Crystal Empire with Rose and Twilight, The Doctor must face his worst enemy.

After returning to Ponyville with Twilight, The Doctor has a vision about something strange in the Crystal Empire, and takes Rose and Twilight there to investigate. But during his investigation, he finds out that he wasn't the only Time-Lord to survive the Time War. When the Crystal Empire is turned upside down, The Doctor, Rose, Twilight and Princess Cadance, must face the Doctor's worst enemy. Who seems to know about The Doctor's future.

Published 2014-11-26 04:50:10 UTC
Last updated 2014-11-26 04:50:10 UTC

Returning to the Present

The Doctor and Twilight ran into the TARDIS quickly closing and locking the doors behind them. “Next time, let’s stay away from southern Equestria.” The Doctor said. “The ponies there are mad.”

“You’re telling me.” Twilight replied. They had traveled back in time to southern Equestria, were the locals, aren’t exactly kind. Especially when you’re a unicorn in an anti-magic society.

“So, were do you want to go next?” The Doctor said cheerfully. “Prehistoric times? The great frontier in the future? No, we can’t take you to the distant future. That would end in disaster.”

“Why would that end in disaster?” Twilight asked.

“Um… Wibley Wobbly Timey Whimey.” The Doctor explained.

“Huh?” Twilight asked confused.

“Something happens in the future, that of you found out, could drive you mad!” The Doctor replied.

“Okay.” Twilight said. “But in answer to were to go next, I would like to go home.”

“Home?” The Doctor asked in a ‘seriously?’ tone voice. Twilight nodded sheepishly. “All right, home it is!” The Doctor started fiddling with the TARDIS controls, pressing random buttons. “The same day you left, am I right? Yes, that sounds about good.” The TARDIS began to shake rapidly and rattle and the screeching sound began to appear.

The TARDIS ‘core’ in the middle of the control panel to go up and down with the screeching sound being made. The Doctor had a sign of grief on his face, while Twilight Sparkle smiled with cheerfulness. She was going home.

Rose Tyler sat in her motel room with several thoughts on her mind. When she had told The Doctor that she was staying in Ponyville, he didn’t seem to care. He acted like she didn’t matter to him anymore, like his regeneration had made him more different then when he had regenerated after the battle against the Daleks.

But, Rose couldn’t help missing The Doctor, even if he didn’t miss her. It seemed as though her life had begun to revolve around The Doctor so much, that she couldn’t live without him. And she wondered how she would react to seeing her again. After all, he had loved it when he saw Sarah Jane Smith again, but that had been after years, so would he be happy? Or would he be disappointed? Or would he just not care?

Before Rose could decide she heard a screeching sound. A very familiar screeching sound. Rose stood up with a sign of glee on her face. She looked out her window and saw a blue police box materializing. She stormed out her door and ran down the stairs, tripping over her own hooves. After all she had only been a pony for two and a half weeks.

She ran out the hotel door as The Doctor stepped out of the TARDIS. Rose ran up to him and hugged him. “Rose!” The Doctor said cheerfully. “It’s great to see you again! Long time no see!”

“It’s great to see you too!” Rose said gleefully. “Wait, long time no see? How long have you two been gone?!”

“It’s just a saying.” The Doctor explained.

“We’ve only been gone for two weeks.” Twilight said, steeping out of the TARDIS.

“Okay, I was just making sure.” Rose replied. "Here, it's only been a few hours."

“Anyway, Twilight, you said you wanted to talk to your friends?” The Doctor implied.

“Oh, yes.” Twilight replied. “I’ll go talk to them now.” Twilight turned around and trotted off. The Doctor shut the TARDIS door and leaned up against it, looking Rose right in the eye.

“All right, Rose, what’s on your mind?” The Doctor asked.

“What so you mean?” Rose asked.

“Something is bothering you.” The Doctor explained to Rose what she already knew. “And, I’d like to know what.”

Rose sighed. “When you regenerated, you acted, different.” She explained. “I mean, I was just getting used to you being different, and then you go and change again.”

“Something tells me, that’s not all.” The Doctor implied.

“Well,” Rose began, “When you wanted to travel back in time and I said no, you acted like you didn’t even care. Like I didn’t matter to you, anymore.”

The Doctor placed his hooves on Rose’s. Then he looked her right in the eye. “Rose, you will always matter to me. No matter what happens I will do everything in my power to keep you safe.” Rose smiled, relieved that The Doctor still cared about her. “Let’s go meet up with Twilight.” Rose nodded. “Come along Rose!”

Author's Note

Anypony getting the feels yet?

Twilight talks about Time Travel

Twilight talks about Time Travel

"And that's when we met Star Swirl the Bearded and helped him defeat an alien called a Weeping Angel and then we went to the beginning of Equestria and actually saw first hoof the play we put on for Hearths Warming Eve every year, and..."

"LAME!!!" Rainbow Dash shouted interrupting Twilight. "Who cares about what happened in the past, we already know what did happen, I want know what will happen! Like if a become a Wonderbolt!" Every one of Twilight's closest friends was gathered in the library listening to Twilight explaining her adventures with The Doctor.

"The Doctor said that we couldn't go into the future, just return to the present." Twilight explained.

"Are you sayin' that he can travel anywhere in time an' space, but he can't go into the future?" Applejack asked.

"He can go into the the future, he just chooses not to with me." Twilight said.

"Whatever for darling?" Rarity asked.

"He says it's..."

"Spoilers." A voice said behind them. Everypony turned around to see The Doctor and Rose standing in the doorway. "If told you about your personal future, it could rip a hole in the fabric of reality and turn the entire universe inside out."

"I didn't understand a single word you just said, but okay." Rainbow said.

"Besides the past is much more interesting." The Doctor said. You get to see things first hoof instead of just hearing about it." The Doctor said.

"I'd still rather see if I become a Wonderbolt." Rainbow Dash replied.

"But where should we go next?" Rose asked.

"I'm not sure." Twilight said.

The Doctor thought for a moment thinking about all the different events that would be fun to see. "I know!" he shouted. "We could see the royal pony sisters in their hay day!"

"That sounds like fun!" Twilight said.

"Oooh! Can I come?" Pinkie Pie asked.

"Why would you want to come?" Rainbow asked.

"Because it's fun!" Pinkie said excitedly.

"Okay, who else wants to come?" The Doctor asked.

"It sounds amazing!"

"Lame, but okay."

"Why not?"

"Um, okay..."

"Well then," The Doctor began. "Let's go see the princesses!"

The Doctor began to trot out the door when Pinkie Pie stopped him. "We can't go without having a party first!"

"All right, a party sounds good." The Doctor said. "I'll be right back." The Doctor left the library and came back with a banana.

"Uh, why do have a banana?" Applejack asked.

"I always bring a banana to a party." The Doctor replied.

"Nice," Applejack said, "Well, I always bring an apple to a party." Applejack removed her hat and pulled an apple out of it.

"I prefer bananas. Bananas are cool." The Doctor said.

"Eh, suit yourself." Applejack said, and took a bite out of her apple.

"Come on everypony, lets get ready to part-A!" Pinkie Pie said, and started the song Shake your Tail.

The ponies started to dance. The Doctor was standing on his back legs and was waving his hooves over his head like a maniac. "Come on Rose, do the drunk giraffe!" The Doctor shouted.

"No, that's embarrassing!" Rose laughed. Pinkie Pie ran up to The Doctor and started to do the drunk giraffe as well.

Once the song ended, Pinkie went over to play the next song. Twilight wanted to walk over to The Doctor and asked if he wanted some cake.

The Doctor took a bite out of the cake and spit it out. "Whats wrong with the cake?" Twilight asked.

"I don't like cake, can you get me something else?" The Doctor asked.

"Sure. What would you like?" Twilight asked.

"Can you get me fish fingers and custard?" The Doctor asked.

"Fish fingers and what?" Twilight wondered.

"Custard." The Doctor said. "Fish fingers and ARGH!!" The Doctor fell on the floor and felt a pain in his stomach, like he was being pulled apart. Suddenly, in his sub-conciseness, he saw a city of crystal. It was under attack, burning in flames melting the crystals into goo. And standing on top of the castle, laughing in triumph was a grey pegasus with a black mane looking over the burning city.

The Doctor came to light with everypony looking at him. He stood up and ran to the TARDIS. "Where are you going?!" Twilight shouted after him. Twilight and Rose ran after him into the TARDIS. "What are you doing?" Twilight asked.

The Doctor pulled a lever on the TARDIS control panel and said, "The trip to the young princesses will have to wait. We have to go to the Crystal Empire."

Capture in the Crystal Empire

The TARDIS evaporated in the Crystal Empire and The Doctor ran out of it looking around at the city. "So, why are we here?" Twilight asked, walking out of the TARDIS being followed by Rose.

"I had a vision of a gray pegasus looking over The Crystal Empire while it burned." The Doctor replied, scanning the crystals with his sonic screwdriver.

"While it burned?" Rose asked. "What do you mean?"

"While it burned, you know, on fire, blowing up, ka-boom. How can I get more specific?" The Doctor said, rolling his eyes. "But who has the strength to blow up an entire city made out of indestructible crystal?"

"Well, the last time I was here, it was to stop an evil unicorn ghost named King Sombra." Twilight explained. "We defeated him using an old relic called the Crystal Heart. My sister in-law Princess Cadence rallied the Crystal Ponies into using their cheerfulness to power the Crystal Heart, defeating King Sombra."

The Doctor turned to face Twilight. "Princess Cadence?" He asked. "Who's she?"

"She's Princess Celestia's niece, and my sister in-law." Twilight replied. "She's married to my brother Shining Armor. You know, I guess that means Princess Celestia is my aunt in-law, or something. Never mind, it's too complicated."

"Where would she be now?" Rose asked.

"Probably in the Crystal Castle Throne Room, performing her royal duties." Twilight said.

"Then that's where we have to go." The Doctor said. "If anything strange has been going on, she'll know."

Twilight showed the way to the Crystal Castle, which wasn't very difficult as it's located in the center of the city. Upon arrival, Rose commented, "It's looks like the Eiffel Tower."

Twilight cocked her head to the side. "What's the Eiffel Tower?" She asked.

"It's a tower in a city called Paris." The Doctor replied.

"I don't know what that is, but okay." Twilight said. They walked into the castle and into the throne room, but what they was not what they expected.

No pony was sitting in the throne, nor anywhere near it. Instead, Shining Armor and several crystal pony guards were standing next to the throne, chatting up a storm.

"But how could she just disappear!?" Shining Armor asked, with a severe tone of anger in his voice.

"I don't know, your highness." A red crystal unicorn replied, stuttering. "I was simply doing my job, giving her the daily work, when she was surrounded by a red explosion. Then she screamed and disappeared. There was nothing I could do."

"That doesn't cut it Firebrand!" Shining Armor shouted, stepping back. "How could you know there was nothing you could do?! Couldn't you perform a spell, or grab her, or..."

"He's a soldier! What do you expect?!" The Doctor shouted. "They don't think about a solution they just shoot things, and then think, and even then, they don't think."

"Who are you, and who let you in?" Shining Armor asked.

"I'm The Doctor, and your sister let me in." The Doctor replied, and walked off to the throne.

"Twily?" Shining Armor asked. "What are you doing here and who are you're friends?"

"Well, this is The Doctor, and this is Rose." Twilight explained. "We met a little bit ago, but they showed that they had abilities unlike any other pony I've ever met."

"So, is he your colt-friend?" Shining Armor asked.

"What?! No! He's just a friend!" Twilight yelled.

"Okay, sorry I'm just in a bad mood." Shining Armor replied. "Something has happened to Cadence."

"What's happened?" Rose asked.

"Some sort of teleportation spell." Shining Armor explained. "And a very talented pony must have conjured it, for it left no magical trace."

"Of course it left no magical trace!" The Doctor exclaimed. and slid down the carpet on the throne.

"What do you mean?" Twilight asked.

The Doctor removed the cushion on the throne and tossed it aside. What was revealed was a flat, metal, circular object with a glowing blue light on it. "A teleport." The Doctor said.

"But, I've seen a teleport before, it doesn't create an explosion." Rose said.

"Excellent question." The Doctor said. "Have any of you noticed that the throne and the area around the throne is a little darker than usual?" The Doctor trotted up to the throne and whipped his hoof across the chair. when he lifted it up a thin layer of black dots was on it. "There's a thin layer of ash on it. It wasn't a spell Firebrand saw, it was just a fancy firework."

"So what did happen to Cadence?" Shining Armor asked.

"When she stepped on her throne a timer was started, so that in an hour she'd teleport. Then a explosion was caused at the same time and she teleported to a different location." The Doctor explained.

"But where did she teleport to?" Twilight asked.

"Only one way to find out." The Doctor said. "Geronimo!" Then he ran towards the teleport.

"DOCTOR DON'T!!!" Rose, and Twilight yelled simultaneously.

Then The Doctor ran onto the teleport, and disappeared.

A Villians Reveal

"Well, your friend's an idiot." Shining Armor said. He, Rose and Twilight were in Shining Armor quarters, debeating what they should do next.

"Well, the way he sees it, if you run straight into trouble, you have the element of surprise." Rose said, who was eating a hay sandwich. "You know, with what I normally am, I don't eat hay, but, surprisingly it tastes good."

"The Doctor might be in danger, and your worried about food?" Twilight asked, looking up from the book she was reading.

"Oi, your reading!" Rose counter-argued.

"I'm researching old enemies of the Crystal Empire." Twilight replied. "It's possible one of them has returned seeking revenge. Again."

"But, that doesn't make any sense." Rose said. "The technology that was used, hasn't been invented in Equestria. I have a feeling it's one of The Doctor's enemies."

"What do you mean, 'The Doctor's enemies?" Shining Armor asked. "Who is he anyway?"

Before Twilight, or Rose could reply, an earthquake rattled the castle.

"That wasn't a natural earthquake." Twilight said. "I think conversation will have to wait, brother. We have bigger problems on our hooves."

The Doctor appeared in a dark rectangular concrete room, with tubes on the ceiling. The air was steamy, as if there was an open sauna nearby. It looked like those rooms you see in movies that are in an industrial stage.

`He walked through the room, and reach a hallway. In the next room, he saw a pool of boiling water. Or, at least The Doctor thought it was water. As he took a closer look, the water had a whitish tint, as if someone put white food coloring into it.

The Doctor pulled out his sonic screwdriver and cooled down a section of the water. He stuck his hoof into the water and quickly pulled it out. The water dripped of his hoof and then form an exact replica of his hoof. "Cloning water, of course." The Doctor said to himself.

Suddenly, the hoof replica lunged at him. The Doctor was sent backwards and fought the cloned hoof. He threw it to his left, and used his screwdriver to turn it back into water. "Controlled cloning water." The Doctor said. "That's a new one."

"Very good Doctor!" A voice from behind The Doctor said. "Though you managed to miss the one thing that actually matters!"

"And what might that be?" The Doctor asked, turning around.

"Who it is that created the cloning water." Then, he stepped out of the shadows. A grey pegasus with a black mane. His cutie mark was an hourglass, just like The Doctor's.

"You're a Time-Lord." The Doctor said.

"Oh, very observant!" The pegasus exclaimed. "I was a Time-Lady, but then you vaporized me, and I was sent to this world, where I regenerated. You've changed too, the last time I met you, you were a old, raving Scotsman."

"Well, thanks for telling me about my future." The Doctor said.

"I beg your pardon?" The pegasus asked.

"I've never been an old raving Scotsman." The Doctor said.

"Oh well, I guess I picked you up a little too early." The pegasus asked.

"What do you mean?" The Doctor asked.

"I brought you here." The pegasus said. "And, your companion. And also a few of you enemies."

"Why would you do that?" The Doctor asked.

"Because I like to see you DANCE!!!" The pegasus shouted.

"How did you bring me here?" The Doctor asked.

"Why do you ask so many questions?!" The pegasus yelled. "But if you want to see how, follow me." The pegasus guided The Doctor through the hallway and into a room filled with computer screens. "I recreated the Time Scoop." The pegasus said.

"What?" The Doctor asked.

"I recreated the Time Scoop, and almost caught pneumonoultramicroscopicsilicovolcanokoniosis creating it." The pegasus repeated. "You remember that thing that The Lord President used to bring four variants of you to the Death Zone on Gallifrey? That was a fun adventure wasn't it?"

"You talk about it like you were there." The Doctor said.

"That's because I was there." The pegasus admitted.

"Wait that means you're..." The Doctor began.

"Finally he figures it out!" The pegasus shouted. "I am you worst enemy, you arch nemesis, I am..."

"The Master." The Doctor finished.

"Yes, Doctor." The Master said. "And I think your going I'm going to enjoy keeping you here as my pet, while I destroy the universe. Ta-ta." The Master walked out of the room and locked the door behind him.

"MASTER!!!" The Doctor shouted.

"Oh, don't worry, I won't kill you." The Master shouted, through the door. "I just want you to watch. Oh, and don't try to get out, it's deadlocked."

The Doctor kicked the door as hard as he could. "YOWZA!!!" He shrieked, and cradled his hoof.

Suddenly, The Master's face appeared on the biggest computer screen. "Ah ha!!! Sorry, I'm so changeable! I will kill you now!" The Master cackled. "What, should we say, death by gas?" Out of the vents, green gas began to enter the room. "Have a good death!"

Author's Note

If you need a voice for this master, just imagine Moriarty from Sherlock.

The Master Plan

"I'll have to thank The Master for giving me a slow death." The Doctor said to himself. He reach into his collar and pulled out a TARDIS key. He closed his eyes. He thought about the TARDIS dematerializing around him. He opened his eyes and he was inside the TARDIS. "Wow, that actually worked." The Doctor said to himself. He grabbed a lever and pulled it.

The TARDIS materialized outside the gas-filled room. The Doctor walked out, and thought to himself, I have to find Princess Cadence. If I don't, her husband will kill me, and I'm running out of regenerations.

The Doctor walked through the hallways knocking on each door he found. In one hall, on the first door to the left he heard a faint voice say, "help." It was a girls voice.

"Hello is anyone in there?!" The Doctor shouted.

"Huh?" The voice said. "Who's there?"

"I'm The Doctor, I'm here to help." The Doctor replied. He pulled out his sonic screwdriver and unlocked the door. He ran into the room. Lying in a bench was a light pink alicorn with a long purple mane, with pink and white streaks. Her cutie mark was a crystal heart. "You must be Princess Cadence." The Doctor said.

"What gave it away?" Cadence asked.

"Everything." The Doctor replied. "Your highness, what happened to you after you were taken captive?"

"I almost drowned in white water." Cadence explained. "Then I was put in here. I've been attacking the door with spells, but nothing seems to have any affect. Not even my obliteration spell."

"There must be a magical damper on the door." The Doctor said, "The Master has gotten clever, really clever."

"Just one other thing." Cadence said.

"What's that?" The Doctor asked.

"Can we leave?" Cadence asked in return. "After all, I'd like to stop this guy, and see my husband."

"Yes, we can leave." The Doctor said. Suddenly, an earthquake began to shake the underground complex. Dust fell from the ceiling, and the bed in the cell toppled over. "Basically, run."

Cadence and The Doctor ran through the complex, until they reached a fork in the road. Cadence went one way, The Doctor went the other. "Where are you going!?" Cadence shouted, over the rumbling noise. "The exit is this way!"

"I have a quicker way!" The Doctor yelled back and continued to run. Cadence sighed and ran after him.

They reached the TARDIS, when Cadence stopped in her tracks. "That's your big escape?" She asked. "A wooden box?"

"Oh, why does this always happen?" The Doctor said to himself. He unlocked the door, and shoved Cadence in the box. The Doctor followed and raced to the TARDIS controls.

Cadence was at a loss for words. She had been captured by a changeling, saved an empire from a 2000 year old ghost, but this box was the most remarkable thing she had ever seen. "It's..."

"Yes, it's bigger on the inside, why is everyone always surprised?" The Doctor groaned. He pulled a lever and the TARDIS core began to go up and down.

Suddenly the core stopped moving, and sparks flew from it. The controls shattered and exploded, followed by a severe rattling. The TARDIS began to shake rapidly, and the typical screeching noise was sputtering, like a car that would start. "What's going on?!" Cadence shouted, being flung to the wall.

The Doctor hung on to the control panel, looking at the remains of the computer screen. "Time block!" He shouted back. "The Master must have become more clever than even me!"

Cadence, flying up to The Doctor, yelled, "What does that mean?!"

"It means we're going to the past!" The Doctor shouted. "The very distant past!"

A Not-So-Simple Solution

"We're crashing!" The Doctor shouted over the exploding TARDIS.

"No, you think?!" Cadence shouted back. She was clinging on to one of the coral-like columns. "Where are we crashing?"

"The proper question, is when are we!" The Doctor yelled.

Cadence rolled her eyes. "Okay, when are we!?"

"About, thirteen hundred years into the past!" The Doctor replied. "Give a take or century!"

"Where thirteen hundred years ago?" Cadence asked.

The Doctor looked at what was left of the computer screen. "The Everfree Forest!"

The TARDIS console shattered even more. The TARDIS itself began to rotate around. The Doctor and Cadence lost their grip and fell onto the floor, and then onto the ceiling. The TARDIS crashed onto the ground with a loud BOOM!!!, and The Doctor and Cadence fell to the floor, and collapsed.

Then the TARDIS sprinkler system went off. "Oh, now you go off!" The Doctor shouted. "Why couldn't you have off five minutes ago!" The Doctor stood up, and kicked the TARDIS wall. He then recoiled in pain. He walked over to the door, and stepped out. The TARDIS was leaning up against a tree, smoke pouring from the light. "Well, the anti-gravs are still working, so it's repairable."

"What's repairable?" Cadence asked, stepping out of the TARDIS. She was soaking wet from the sprinklers.

"The TARDIS." The Doctor replied, drying off his bow-tie. "It can be fixed, so we can go back to the future."

Cadence began to squeeze the water out of her mane. "But who did this?" She asked. "Who is he, and what's his plan?"

"He's called The Master." The Doctor explained, putting his bow-tie back on. "He's an old enemy I thought long dead. The reason he kidnapped you was to create a clone that he could control, but I'm not sure why."

The Doctor looked around his surroundings. The Everfree Forest wasn't like the way it was in the future. It was nice and green, with small insects flying around. It was a bright summers day, around eighty degrees Fahrenheit. But, it smelled wrong. Like a small town. He turned around and saw a bridge over a canyon. Beyond the bridge was a huge castle. The Doctor realized, he was looking at the Castle of the Royal Pony Sisters.

"Oh no..." He muttered to himself.

"What?" Cadence asked. The Doctor ignored her and ran into the TARDIS.

The lights were off, and the sprinklers were off. The Doctor began pressing buttons on the console remains. He got a frustrated look on his face and punched the console. "What's wrong?" Cadence asked, walking into the TARDIS.

"The only power that's left is the emergency power." The Doctor said. "There isn't enough power to travel back through time. The monitor still works at least." He walked over to the monitor and shut it off, trying to save power.

"So we get help." Cadence said.

"From who?" The Doctor asked. "Who in this world would help us?" Suddenly, The Doctor got it, and a grin flashed upon his face. "This is the time of the Royal Pony sisters! We can get their help!"

He open the doors, only to see a spear pointed straight at his face. "Oh, hi." The Doctor said. "I was wondering if you could take me to the princesses." The Doctor was looking at two royal guards, wearing obsidian armor, covering their whole bodies.

"Shut up you!" The guard on the guard on the left said.

"No one trespasses on the princesses territory!" The right guard said.

"Hey, I crashed!" The Doctor exclaimed. "It isn't my fault that it crashed!"

"I told you to shut up!" The left guard shouted.

"Oh, what are you two doing now?" A voice behind the guards said. A dark blue alicorn, with a blue flowing mane stepped up. "We are a welcoming people, why you haven't been fired is beyond me." She said.

"Oh, you're Princess Luna." The Doctor said and bowed. "I was just coming to see you."

"You were?" Luna asked. "Why, pray tell."

"Oh, box issues." The Doctor replied. "You know how it is."

"I'm afraid I don't." Luna said.

"Well, it's a long story," The Doctor began. "But, needless to say, we're from the future?"

Luna raised an eyebrow. "We?"

"Oh, right. Sorry." The Doctor said. "This is Cadence." Cadence stepped out of the TARDIS and shyly waved at Luna.

Luna got a shocked look on her face. "Another alicorn?" She mumbled. "How is this possible?"

"We're from the future." The Doctor explained. "About 1300 years into the future, and if we don't get back soon, I can only imagine what The Master will do."

Luna shook the confused look off her face. "I think you may want to see my sister."

The Throne Room was amazing. It was large, with gray wall, with tapestries lining them. Were Celestia sat was a sun tapestry, and a moon one for Luna. They each sat on a throne at the back of the room, while The Doctor and Cadence looked up at them.

It took a while for Luna to explain what had happened to The Doctor and Cadence. They had told Luna the entire story (mostly) on the way to the castle. Luna hadn't understood all of it, but she got the basic info. "So, you need an energy source to power you machine?" Celestia asked.

"That's right." The Doctor confirmed.

"What kind of power do you need?" Celestia asked again.

"Something stable, that won't burn out the TARDIS power matrix, but powerful enough to get us at least one trip." The Doctor explained.

"Hmmm..." Celestia was thinking of something, but no one was sure what.

After a few minutes of silence, Cadence spoke up, "So is there any sort of energy that might work?"

"I can not think of any." Celestia said calmly.

The usual grin that was on The Doctor's face melted off, and a scowl formed. "Oh, come on!" He shouted. "Do you really think that that will do?"

"I beg your pardon?" Celestia asked.

"This is your land in danger!" The Doctor exclaimed. "If you can't help us, it will be destroyed!"

"I'm sorry, brave colt, but there is no such power source that you seek." Celestia said. She said everything calmly, like she didn't care about the future.

Luna had heard enough. She had an idea, though it would be tricky. "I believe I have a solution." Luna said.

"I'm listening." Celestia replied.

"Magic is the solution." Luna explained. "More specifically, alicorn magic. It isn't capable of being destroyed, and it is powerful, but certainly not as powerful as emotional magic, such as love and friendship magic."

"That may work." Celestia agreed. "But, it would take a considerable amount of magic. You couldn't do it alone, you entire life force may be drained out. Even together, we may not have enough strength."

"What about a third element?" Cadence asked. "I'm an alicorn too, after all, it may work with three of us."

Luna nodded and looked at Celestia. Celestia sighed and said, "It's worth a try."

The Doctor had hooked up cables to the princesses. Luna and Celestia were outside the TARDIS, while Cadence was inside. The Doctor had set the coordinates, as once there was enough energy, the TARDIS would wake up and travel to where it was set to go. The Doctor had it set up to where it would appear about five minutes after they left.

"Are you sure of this sister?" Celestia asked.

"No," Luna admitted, "but, if it's the only way to save the future, we must try."

Celestia nodded. "Then I trust you."

The Doctor poked his head out the doors of the TARDIS. "Two things: first of all, when I shout now, start producing as much magic as you can muster. Also, find a forth alicorn princess." The Doctor ran back in, and started to prepare the wrecked TARDIS. It wasn't easy with a half-exploded console.

He turned to Cadence. "Ready?" He said.

She smirked and replied, "Ready."

The Doctor took in a deep breath and shouted, "NOW!!!"

Immediately, the alicorns began to produce magic. The TARDIS power was slowly being restored. The Doctor activated the computer screen and looked at the power levels. 35% AND RISING it read. The power levels increased more, and more. All the TARDIS needed was 75% and it would start going. 50% AND RISING. "Just a little more. 74% AND RISING. The lights came back on, the central core began to move up and down, and the power levels reached 75%. The Doctor's laugh rang throughout the busted time-machine, and it dematerialized into the time vortex.

The Last Skirmish

Shining Armor stared at the pink pony in front of him. It was Cadence, yet at the same time it wasn't Cadence. She had a blank look on her face, like she was watching a game that she didn't care about. Her eyes were droopy, and her mouth was straight. She looked completely emotionless.

"Well then, "the pegasus said, "I must be off. Toodle-oo!" He spread his wings and took off.

"Wait!" Twilight shouted. The pegasus looked behind him. "Who are you?" Twilight asked.

The pegasus smiled. "My name is The Master." He turned around and flew to the weapon.

Shining Armor still gazed at the alicorn that was staring back at him. Cadence stared back at him. "Cadence, can you hear me?" Shining Armor asked. "Do you remember me?" Cadence still looked at him blankly, as if his words didn't even register. "Are you all right?

All of the sudden, Cadence looked up. Her eyes widened. When she spoke, it sounded mechanical. "Orders received." Cadence said. "Destroy Shining Armor, Twilight Sparkle, and Rose Tyler." Cadence's horn lit a light blue, and a wave of energy was hurled at the ponies. They were sent flying into the pedestal holding the Crystal Heart.

When they stood up Twilight pointed to the Crystal heart. "Look." She said. The Crystal heart was becoming a darker shade of blue, and it was beginning to crack. "The Master wasn't kidding when he was drawing energy from the Crystal Heart."

"It's breaking." Rose said. "What happens if it does break?"

"I don't know." Twilight acknowledged. "The Crystal Heart is one of the most powerful artifacts in existence, next to the Elements if Harmony. If it were to be destroyed, it could unleash a wave of energy destroying everything in a twenty mile radius."

"So we have to stop it from being destroyed." Rose said.

"We have to stop that weapon from firing." Twilight said "Even if the Crystal Heart get destroyed, the weapon will destroy the entire universe! And, I have a feeling if we destroy that weapon, we will save the Crystal Heart."

"Than that's what we have to do." Rose agreed.

"How could she do this?" Shining Armor asked. He was staring at Cadence, with his mouth wide open.

Twilight placed her hoof on his shoulder. "Shining Armor." She said. He turned his head to look at Twilight. There were tears in his eyes. "I don't think that is Cadence. I was fooled once into believing that someone was the real Cadence when they were a fake. I won't be fooled again. And neither should you. You know Cadence better than anyone, look me at her, look at how emotionless she is. Now look me in the eye and tell me that's the real Cadence."

"I...I can't." Shining Armor said.

"Then what does that tell you?" Twilight asked.

Shining Armor didn't even need to answer. His expression said everything. He stood up and hugged Twilight. "Thank you, Twily." He said.

Twilight hugged him back. "You welcome BBBFF."

Rose perked up. "I don't mean to interrupt the moment, but you may want do duck." Twilight and Shining Armor looked up and saw Cadence lunging at them. They ducked quickly as Cadence slammed head first in the Crystal Heart. It cracked even more.

The three ponies ran to the other side of the courtyard as Cadence tried to regain her balance. "So what's the plan?" Shining Armor asked.

"We have to hold off Cadence, and defeat The Master before time runs out!" Twilight said.

"How much time to we got left?" Rose asked.

"Judging by the damage already done to the Crystal Heart, about ten minutes." Twilight said. "I'll teleport up to the top to the tower and face The Master, you two try to hold off Cadence!"

"Got it!" Shining Armor acknowledged.

"Good." Twilight's horn shone purple and she teleported to the tower.

At the top of the tower, The Master turned around and saw Twilight. Her mane was waving in the wind. "Well, well, well, what do we have here?" The Master asked.

"You will not succeed Master." Twilight said.

"Won't I?" The Master asked. "The Doctor isn't here, is he? He's the only one who could ever stop me, and right now, he's stuck in the past!"

"What so you mean?" Twilight asked.

"I sent him and that stupid princess back in time!" The Master cackled. "And his TARDIS was damaged beyond repair! There is no chance in seeing The Doctor again!"

"He could figure out a solution!" Twilight responded. "He can always get out of a tight spot!"

"Not this one, sister!" The Master shouted. "Trust me, you will never see you little Doctor again!"

Then a sound broke the air. A groaning, wheezing sound. Then a light struck to the right of the tower. The TARDIS appeared, spinning out of control. Smoke poured out of it as it hit the tower. The top light was on fire.

The doors opened, and Cadence flew out of the TARDIS crashing into the false Cadence. The two matching ponies fell onto the pavement, and began to hit each other.

Meanwhile, the TARDIS was still spinning out of control. It came to the top of the tower and began to fall again. The doors opened and The Doctor jumped out onto the ledge where The Master and Twilight were standing, leaving the TARDIS to crash down onto the ground below.

"Oh, big, big mistake, really huge." The Doctor began. The Master began to back up. "Didn't anyone ever tell you there's one thing you never put in a trap, if you're smart, if you value your continued existence, if you have any plans about seeing tomorrow, there's one thing you never, ever put in a trap!"

"And what might that be?" The Master asked.

The Doctor looked straight into The Master's eyes, anger burning in his own. "Me." The Doctor whipped out his sonic screwdriver, and used it on the control panel. A series of sparks and sizzle came from it.

"No!" The Master shrieked.

The Doctor put his sonic away and told Twilight, "That, is how to take care of business." Although, victory was short lived, as the machine, kept drawing power from the Crystal Heart.

"What?!" The Doctor asked.

"Oh, how I love trolling you!" The Master said with glee. "It's deadlocked! A simple little screwdriver won't stop it! I know we went to the same academy, but you are such an idiot!"

"No." The Doctor mumbled. "There must be a way to stop it, there always is."

"Not this time." The Master said.

"There's only seven minutes left." Twilight whispered in The Doctor's ear.

"Come on!" The Master shouted. "I know you want to defeat me, you just don't know how!"

"There has to be a way!" The Doctor shouted back. "I need to think." The Doctor mumbled to himself, while he started pacing. "The weapon can't be stopped, so it has to be blocked or absorbed by something, something of infinite mass and size, like another universe, of a..." His voice trailed away. "OF COURSE!!!" The Doctor shouted as loud as he could. "That's it!"

"What's it?!" Twilight asked.

"The TARDIS!" The Doctor shouted gleefully. "Teleport us to the ground." Twilight did so leaving The Master with a confused look on his face.

The authentic Cadence was still fighting the deceptive Cadence, as The Doctor grabbed Rose and ran into the TARDIS. "What did you do to it?" Rose asked, as soon as they stepped into the time machine.

"The Master did it, not me." The Doctor replied, and he began to press buttons on the remains of the console.

"What are you doing?" Twilight asked.

"I'm setting up the TARDIS to where it will fly right above the weapon." The Doctor explained.

"What?!" Rose shouted. "Why?"

"Because," The Doctor began. "In order for the weapon to be stopped the blast of energy has to be absorbed by something, something of infinite mass and quantity. The TARDIS is the only thing that fits the bill."

"But, it will destroy the TARDIS, won't it?" Rose asked.

"No, that's the beauty of it." The Doctor said. "It will absorb the energy, repowering the TARDIS. Also, the TARDIS will have so much power, it will return to the universe from which it originated. It will rip a hole into the universe, and send the TARDIS, Rose, and I back home."

"Really?" Rose asked. "We can go home?"

The Doctor nodded. "Yes." He said. "We will return to the same moment in which we left. One last thing: I will return to my previous regeneration. I'll go back to the man in a tight suit, with amazing hair."

"You'll go back to being you?" Rose asked.

"Yep." The Doctor confirmed. "This regeneration won't count."

"Well then what are we waiting for?!" Rose shouted. "Let's get to work!" Rose walked up to help The Doctor.

The Doctor looked over to Twilight. She had tears in her eyes. The Doctor walked over to her. "What about The Master and his weapon?" She said, fighting back tears.

"They'll go back to the moment they left from the my universe." The Doctor replied.

"Are you sure you have to go?" Twilight asked.

"I may never get another chance." The Doctor said. "I have to take advantage of it. For Rose's sake."

"I'll never forget you." Twilight said. She looked The Doctor in the eyes and hugged him.

The Doctor pulled out his sonic screwdriver and set it in front of her. "Take it." He said. "You might need it."

Twilight levitated the screwdriver and gave The Doctor one last smile before running out of the TARDIS. She looked behind her, and saw the doors close. The TARDIS began to make it's unique noise, except is was stuttering, like it was dying.

The TARDIS lifted off the ground, spinning up above the tower. It was hovering above the weapon, just waiting for it to fire.

Thirty seconds.

Twilight thought about how the Doctor was saving everyone's lives in this selfless act. How he wasn't even asking for a thank you, he was doing it out of the kindness of his hearts.

Twenty seconds.

The Doctor once said that time was a lifetime, unexplored. He believed that it needed to be seen, it needed to be discovered. But, he let other people see it to, just so they he wasn't alone.

Ten seconds.

He traveled all of space and time, saving it from destruction, form the selfish needs of people. That, is what made The Doctor different. That is what made him a hero.

Times up.

The weapon fired, it a gleam of light, straight at the hovering TARDIS. A bright flash of light covered the entire city, making it impossible to see. Twilight covered her eyes. The bright light shone for several minutes before dying out.

When Twilight opened her eyes, the TARDIS was gone. The weapon had also vanished, along with the Master and the false Cadence. Shining Armor was hugging Cadence and the crystal ponies began to come out of there homes. The battle had ended.

Epilogue

It had been weeks since to ordeal in the Crystal Empire. Since Twilight had come back, she had gotten used to not traveling in time and space, and had gotten comforted by her friends. She still missed The Doctor, and wished she knew what had happened to him and Rose.

She was in a deep sleep when she was woken up by a green light. She thought it might be some of Star Swirl the Bearded notes, which she had gotten before she had gone to bed. She looked downstairs, and saw that it was The Doctor's sonic screwdriver.

She walked down the stairs and touched it. Immediately, a projection of a pony appeared. It took Twilight a moment to realize that it was The Doctor, the way he was when she first met him. He was wearing a regular tie, not the bow-tie she had gotten to.

"Hello? Is anyone there?" The Doctor asked. His voice was back to the way it was before too. "Twilight, can you hear me?"

"Yes. Yes I can hear you!" Twilight said.

"Right." The Doctor said. "Can you see me?"

"Yes I can see you." Twilight replied.

"Good, but, cause you just move into my line of sight a bit?" The Doctor asked. Twilight moved to into the Doctor's vision, so he could see her. "Ah, that's better. Aren't you glad I gave you that screwdriver?"

"Yes, I am glad." Twilight said. "I haven't used it, but I'm glad you called."

"Yep." The Doctor replied. "So, how's life been?"

"It's been fine." Twilight replied. "I've been spending time with my friends a lot, so it's been helping. How's life with you?"

"Not bad. I have a new screwdriver, just like my old one, so I'm going to take Rose to the 1950's to see an Elvis concert." The Doctor said.

"Who?" Twilight asked.

"He's a musician, oh never mind!" The Doctor said.

"I thought you weren't actually a pony." Twilight asked.

"I'm not," The Doctor explained, "so I put this transmission through the TARDIS circuitry to give you a familiar face."

"Well, thanks." Twilight said.

"Hang on." The Doctor said. He reached over to something and looked at Twilight. "The transmission is fading, we're running out of time. Is there anything you wanted to ask me?"

"Are you coming back? Will I ever see you again?" Twilight asked.

"Oh, yes." The Doctor replied. "One day, I'll come back, one day. Until then, you must have no regrets, no tears, no anxieties. Go forward in all your beliefs, and prove to me that I am not mistaken in mine." The Doctor smiled at her. "Good bye, Twilight Sparkle." The Doctor's last words were, and then he disappeared.

Twilight looked at were The Doctor had been standing. She walked up to the window, and looked at the sunrise. She was so happy, she just felt like singing. After all, morning in Ponyville shimmers.

Prologue

The Crystal Empire stood as a monument to all that was pure in Equestria. The crystal shone in the light of day as the crystal ponies played in the sunlight. The crystal showed the mood of cheerfulness and excitement with the approaching Equestria Games coming in a few weeks.

The Princess and Prince that ruled the empire were kind and encouraging. They ruled kindly without worry. But unknown to the crystal ponies of the land, beneath the empire, in the catacombs of the lowest kind, a Pegasus was waiting to strike.

He stood in front of several computer screens, watching the land for a certain object to appear. He flexed his wings and breathed heavily. He felt rage, and anger to the world. No, not just the world, he hated the entire universe.

The universe was corrupt and distrusting. Destruction rained everywhere with all of the great species destroying themselves in pity quarrels and fights. He couldn’t stand it. His race was supposed to be a peaceful race. But as soon as a war was waged, is race turned into warriors and destroyers.

Except him. He had always been a warrior and a ruler. He hated everything and trusted nothing seeing how he had been used. He had been used as a weapon to bring his race back. But, in the end, he destroyed them. All but one.

That one needed to be dealt with. Destroyed and taken care of, in a matter of sense. But, the universe was his primary focus. It needed ruling and restrictions. It required a great cataclysm of creation. And as the blue box appeared, he realized that what the universe really needed, was a master.

Author's Note

For the villain of this story, his timeline takes place after Death in Heavon in Doctor Who. Don't worry it will be explained later how.

The Ultimate Weapon

Twilight, Shining Armor, and Rose ran out of the Crystal Castle, the ground still shaking. "Firebrand!" Shining Armor shouted.

The crystal unicorn ran to Shining Armor. "Sir!" He shouted.

"Tell everypony to stay indoors!" Shining Armor ordered. "Make sure they don't leave!"

"Understood!" Firebrand ran off to the other soldiers.

Suddenly, the rattling stopped. The ground became still. Too still.

"Something isn't right..." Twilight began. Then the top of the Crystal Castle exploded in a fiery blaze. The aurora created by the castle was vaporized in a flash of light and chunks of crystal rained to the ground. Shining Armor created a shield around Twilight, Rose, and himself.

Soon a giant metal pike, extended out of where the castle had exploded. It, than opened into three pieces and a smaller pike extended out of that. A grey pegasus flew out of the castle and flew to the weapon. He flew to a clear area just below the weapon, where the controls were located.

"That must be the pegasus The Doctor was talking about." Rose yelled.

"Of course!" Twilight agreed. "That must be what he uses to destroy the Crystal Empire!"

"Oh, it will destroy the more than the Crystal Empire!" The grey pegasus landed in front of the three ponies. He folded his wings and raised his head. Twilight then noticed his cutie mark was an hourglass, just like The Doctor's.

"What do you mean?" Shining Armor asked, anger apparent in his voice.

"This empire is boring." The pegasus replied. "Why do you like it here? Don't you just want to leave sometimes? Maybe take over a different empire?"

"We didn't take over the empire!" Shining Armor yelled. "It was given to us!"

"Oh, baleks!" The pegasus said. "You just took a crystal heart down to a pedestal, and had everypony follow you."

"Hey, do you think you can just come here and insult me, and get away with it!" Shining Armor yelled.

"Yes." The pegasus answered calmly. "Of course I do. I'm not even a pony citizen. I just live here. Anyway, what this weapon does is channel the energy and magic of the Crystal Heart, to create a huge explosion destroying the entire universe."

"You're insane!" Rose shouted.

"I'm a psychopath, what do you expect?" The pegasus said.

"But, why would you destroy the entire universe?!" Twilight asked.

"I'm bored." The pegasus said. "Sorry, can't talk anymore. I've got a weapon to prep, and you've got a pony to fight."

"Oh, you will get it." Shining Armor said, his horn glowing purple.

"What?" The pegasus asked. "Oh you think you're fighting me?!" He started laughing furiously. "That's rich."

"Wait," Shining Armor began, "if we're not fighting you who are we fighting."

"Your wife."