Doctor Whooves: Crossings of Time

by DarkMasterX

Rating: teen
Tags: My Little Pony: Friendship is Magic, Dark, Original Character, Adventure, Crossover, Doctor Whooves, Main 6
Length: 3667

The Doctor faces a new enemy, or in his case, a very very old one...

After being pulled away from what seemed like the perfect vacation, The Doctor and the gang must face a new enemy!

This story was made for people who know the Doctor Who show on BBC America, criticisms are always welcome!!!

Published 2012-06-10 06:54:02 UTC
Last updated 2012-06-10 06:54:02 UTC

Chapter 1

Twilight held on to the rails as the TARDIS shook and rocked violently. Her, the Mane 6, and the Doctor were going to travel to the planet Midnight, which was supposed to be the best vacation planet. Suddenly, while traveling, the Doctor had lost control and now they all were on this crazy ride. “Doctor what's going on?” Twilight shouted over the beeping and whistling of the TARDIS.

“The TARDIS is flying to a point in time way off course!” The Doctor shouted, moving from control to control.

“So steer it back on course!” Applejack shouted, pressed against a wall.

“She locked the controls!” The Doctor responded, “The only thing I can do is try to smooth out the ride.”

“You call this smooth?!?” Rainbow Dash asked, trying to hold her position on the ground against the shaking.

“It's fun!” Pinkie Pie said, not seeming to notice the rocking, “Like a roller coaster!” With a shudder and a powerful jolt the TARDIS finally came to a halt, causing everypony to fall.

“Well, that was certainly quite the ride.” Rarity said, picking herself up and dusting herself off.

The Doctor went back to the controls, “She's still locked.” he reported, then more quietly, “What's wrong girl?” He checked the monitor, “She's sent us back to Ponyville,” The Doctor said, “only five days after we 'left'.”

“Why?” Twilight asked, helping Fluttershy to her hooves.

“No idea,” the Doctor said gravely, “But whatever the reason is, she knows we have to be here right now.” The Doctor pressed a few buttons and headed outside, the Mane 6 following hurriedly. Outside everything looked fine: trees swayed in the wind, flowers bloomed cheerfully, and the sun shone brightly. As soon as the last of the ponies left the TARDIS, it suddenly faded out of existence.

“Doctor!” Twilight shouted out alarmed.

“Not to worry,” The Doctor responded, not turning to look, “I set her to lock herself on one particular second, I'll get her back when we solve the problem.”

“Um...Doctor? Everything looks fine.” Applejack said, several ponies nodding in agreement.

“Really?” The Doctor asked, “Nopony notices anything?”

“The animals are gone.” Fluttershy whispered, looking around anxiously.

“Exactly.” The Doctor said, “Not a twitter, nor a peep, not even a rustle.” He looked around, scanning everything. “All of the animals are holding still, wherever they are.” Everypony stood still, letting those words sink in.

“We have to get to town.” Twilight said.

Everypony walked to town, the Doctor more slowly than the others. Twilight paced herself until she was walking next to the Doctor. “Is there something you're not telling us Doctor?” Twilight asked.

The Doctor looked at her, hesitated, then said, “While on the TARDIS, I felt something from her, something I hadn't felt in a long time.”

“What?” Twilight asked.

“Fear.” The Doctor said, “Whatever is going to happen, the TARDIS has a hunch, and doesn't like it.”

Twilight stared at him and said, “If theirs anything I've learned traveling with you, It's that you always find a way to fix any problem, and I don't have to be afraid.” The Doctor looked at her and gave a little, reassured smile. Twilight, satisfied, walked ahead with the rest of the group.

The Doctor frowned as she walked with the group, “I don't think I can this time.” he whispered silently.

**************

They reached town and were surprised to see everything seemed alright. Ponies were talking and walking, stores were open, as if nothing was going to happen. “Granny Smith!” Applejack called out. An old green pony turned around and smiled.

“Howdy-do Applejack!” she called. Everypony walked up to meet the old pony.

“Has anything happened since we left?” The Doctor asked abruptly before anyone had the chance to speak.

Granny Smith, after a pause said, “I don't think...”
“Anything at all?” The Doctor pressed, “Anything slightly different or somepony new in town?”

Granny Smith's eyes lit up, “Oh, that nice gentlepony.”

“What gentlepony?” The Doctor asked.

Granny Smith thought for a moment, “He came into town earlier today.” she said, “He was very polite, complimenting everyone on random things. He asked where the train station was and went that way.”

“What did he look like?” The Doctor asked.

“He was a unicorn,” Granny Smith said, “Black, smoothed back mane, black flank, but the eyes,” Granny Smith paused, “he had red, piercing eyes with a terrible look behind them. Like a terrible hunger for something.”

“What about his cutie mark?” Twilight asked.

Granny Smith thought for a minute, “It was a...looked like a...” she licked her lips in thought, “What was that called...?” The group turned to leave and Granny Smith suddenly jumped, “That's it!” Everypony turned again and she pointed at the Doctor, “It looked like yours!” The Doctor froze, seemingly in shock.

“When's the train leaving?” Twilight asked.

Granny Smith thought again, “It should be leaving soon.”

The Doctor bolted in the direction of the train and, with a hurried thanks to granny, the others took after him. They reached the train as the conductor shouted, “ALL ABOARD!!!” The Doctor ran to a window where the pony seemed to be sitting. The pony turned towards the Doctor and they stared at each other. The pony on the train smiled as the train started to depart.

As the train left the Doctor turned to Twilight, “Can you teleport us to Canterlot?”

Twilight, a little shocked at the harshness in the Doctor's voice, said, “Well, I've never tried to teleport with so many ponies before. I don't think I can.”

The Doctor paced for a second then looked at the group. “We need something that can get us to Canterlot fast.”

Pinkie jumped up excitedly, “Oh oh oh I know!” she said, “A hot air balloon.”

The Doctor looked at her. “Where did you get a...? Never mind. We need it now!”

*****************

A few moments later, the team, aside from Rainbow Dash, who decided to fly alongside, was on the balloon and flying towards Canterlot. “Doctor, what's so important about this pony?” Twilight asked, “Sure he's new in town but-”

“Twilight,” the Doctor interrupted, “cutie marks represent something somepony is good at. If he didn't have a similar cutie mark, I may have brushed him aside. No one can be good with time but me.”

“But-”

“Even if all of this was a coincidence,” the Doctor continued, “I could feel it. That pony is a Time Lord.”

Everything seemed to stand still at this information. “But that's good, isn't it?” Twilight asked, “Someone you know is alive.”

The Doctor hesitated, “He's not who I think he is, but I can tell he's up to something bad.”

“I could too.” Fluttershy whispered, “He made me feel wrong.”

The Doctor looked at the rapidly approaching city, “Whatever he's doing here, it's going to be very big, and it's going to be very bad.” They departed from the balloon as quickly as they could. The pony was nowhere to be seen. Rainbow suggested flying over the city to look for him but the Doctor waved her down. “I know where he's going.” he said and he started running.

By the time the team realized where they were going, they were there, outside of the palace. “Impossible.” Twilight said, but the Doctor was already walking in past the guards, who let him through. The rest followed and they entered the main hall where the pony was talking to the princess.

“Princess,” the pony said, “I think I'm asking for a fair trade.”

“You want me to give you the Elements of Harmony? Even if you were giving me something for them I would still decline.”

The pony twitched his head, “Princess,” he said, “you don't seem to know who I am, what I am.” He then paused, “But no need to worry,” he said, then he turned towards the team, “because the hero is here!”

Celestia looked at them, “Doctor, who is this pony?”

The Doctor stepped forward, “I wish I knew.”

The pony laughed, stepping towards the Doctor, “He doesn't remember, I'm hurt.” Then he paused and looked at the Doctor, “You couldn't remember me.”

“I'm sorry,” the Doctor said, “I don't, but you must be amazing if you survived the war.”

The pony laughed, “I'm not a survivor, I'm a winner.” The Doctor froze, he recognized that phrase. “Impossible.” He said, stepping back.

“Doctor,” Twilight said, “who is he.”

The pony looked at the Mane 6, “Well it's simple,” he said, “I'm The Doctor.”

Everyone froze and tried to process this information. “Impossible.” Twilight said.

The pony smiled, “Nothing's impossible,” he said, “just improbable.”

The Doctor shook his head, “How?” he asked, “Wormhole, a crack in realities?”

The pony smiled coldly, “Much more sinister than that.”

“Do you remember the planet Messaline, Doctor? The Hath and human war? You daughter made from your DNA?” The Doctor took a sharp intake of breath. “I thought so,” The pony continued, “the war was over and the races at peace. The machines were discarded, but not the DNA. The DNA sat in the machine, waiting to be used. A group of robotic scavengers found the machine and extracted your DNA. Once they had it, they tried to recreate you, but failed. You couldn't survive outside of a medical unit and they tortured you for centuries.” The Doctor looked at him in horror.

“I was born from hatred and helped you realize, no one is ever there for you, just yourself. I helped you, let your hatred fill you and, when you finally got the chance, you died and I was born. The regeneration was new and unexpected, but necessary. I had the strength to escape and destroy those scavengers, then looked for the one person I hated most of all, you.

Imagine my surprise when I discovered you had just disappeared. It took me forever to get to this dimension and track you to this planet. So here we are” The pony concluded.

The room was silent. The Doctor stepped towards the pony, “I understand your hatred,” he said, “and I can sympathize. But leave these ponies alone, your quarrel is with me.”

The pony laughed, maniacally, “That's what I thought too,” he said, “but then I realized: I'm not here to kill you, but to help our species.”

The Doctor stared, “How?”

The pony smiled, “No spoilers.” He turned to the Princess, “Now about those Elements-”

“You'll never receive them.” She said.

The pony frowned, then sighed. “If I can't convince you nicely, I'll have to be mean.” He turned towards the group, “I know your looking for a way to stop me, but you can't. I can't lose.” Rainbow Dash sped towards him and the pony flicked a hoof. Rainbow fell to the ground, smoke rising from her wing.

“Rainbow!” Twilight yelled, running towards her. Twilight checked her wing and found a small hole. The Doctor turned angrily towards the pony, who held the item he had aloft.

“It's a laser screwdriver.” he explained, “Much more advanced than a sonic, and much more effective.”

“You're not the Doctor.” Fluttershy said, her voice rising, “You can't be the Doctor or anything like him. So you CAN'T BEAT HIM!!!” she screamed the last words.

The pony frowned coldly, “No. I'm not the Doctor and never will be. I am better. I am supremacy. I am The Time Lord Victorious.” He turned towards the Princess, “And I...never...lose.”

Victorious held up the screwdriver and pressed a button. A beam came out and hit Twilight in the chest. “Twilight!” Celestia shouted. Victorious aimed again and blasted Applejack, who had tried to charge at him.

“The beam is on low,” he said, blasting the Doctor, “but I can turn it up higher.”

“No...stop.” Celestia said as Rarity crumpled to the floor.

Victorious aimed at Fluttershy, “You know what I want.”

“Fine! Just stop!” Celestia said, “The Elements are yours.” Using her magic she opened a door and pulled out a chest. She gave it to Victorious, who opened it greedily.

“This is fine.” he said, then he looked at Fluttershy. “Your friends are unconscious, treat them well and they'll be fine.” With that he teleported away, leaving the pony to take care of her friends.
******************

The Doctor opened his eyes and remembered what happened. He jolted up and surveyed the scene. Twilight and Rainbow Dash were awake and Fluttershy was taking care of the others. The Doctor rose and headed for the door but Twilight headed him off. “Where do you think your going?” she asked.

“To find Victorious.” the Doctor said, trying to move past her but she held out a hoof.

“No you're not.” Twilight said, “You're going to wait for the others to wake up then we'll go together.” The Doctor opened his mouth, but Twilight cut him off. “If you try a whole 'It's my fault' speech it won't work. This would have happened anyway. Victorious is cruel and wicked. He would have gotten the Elements anyway.”

“He threatened our Princess and won't get away with it.” Rainbow said. The Doctor looked at them and sighed.

“We need a plan.” Twilight said, looking pointedly at the Doctor.

The Doctor thought, “He's probably going to use the Elements as some kind of conductor,” the Doctor said, “So he'll need a high area, like a mountain.”

“The mountain that dragon was going to sleep in was pretty high.” Twilight said, “That might be our best bet.”
*********************

With everypony awake they all took the hot air balloon to the base of the mountain and climbed the rest of the way. The Doctor stopped outside of the entrance and turned towards the other ponies. “I don't know what he's planning,” he said sternly, “but whatever it is I need you all to listen and do exactly as I say.” Twilight opened her mouth to speak, but the Doctor cut her off, “This can be anything, even if I tell you all to leave me behind and run, to save yourselves and leave me to die.”

The Doctor looked at them all as they stood still in shock. “I need you to swear you all will do this.” he said. Slowly and hesitantly they all agreed. The Doctor turned towards the cave entrance. “Well then,” he said, taking a deep inhale, “Allons-y!”

They entered and there Victorious was, standing in front of a huge machine, the Elements attached to cables. Victorious turned towards the ponies with a smile. “The machine is complete.” he said, “soon all the world will be as it should.”

“What do ya mean 'as it should'?” Rainbow asked.

Victorious turned towards the Doctor, “Figure it out.” he said, simply.

“I don't need to,” the Doctor said, “that's a Time Vortex Defibrillator, able to tear a hole in the fabric of time and space. Your going to rip open the time vortex here?!?”

“No.” Victorious said, “My plan is much more...complex.”

The Doctor looked at the machine, “You're going to move the planet.” he said, “But you need a huge energy source and a ship capable of...” the Doctor's voice trailed off, “You want to steal the TARDIS.”

“Buzz Buzz!” Victorious said.

“But you'd need the TARDIS codes to plug into the machine to even begin moving the planet.” The Doctor paused, “Of which you already have I take?”

“Of course, Doctor.” Victorious said smugly.

“But why?” the Doctor asked, “Why move the planet and open the vortex unless-”

“This is why we are here.” Victorious said, “Why we came to this pathetic planet. These ponies will dematerialize and from the ashes the Time Lords will rise again!”

“But it took several centuries for humans to turn to Time Lords.” The Doctor said, “And several died in the process.”

Victorious nodded, “True a few will die, but the Time Lords will be reborn from this! You can understand this is for the best.”

“It would have worked,” the Doctor said, “if you hadn't been distracted talking to me.” Rainbow Dash and Applejack had snuck behind Victorious and charged the machine. However before they could a bubble appeared and blocked them, making them both fall back.

Victorious laughed, “You think I would leave it defenseless? No. I have learned from others' mistakes, and I have learned from you to always have a companion waiting to assist you.” He gestured theatrically, “May I present mine!”

A pony stepped from the deeper part of the cave and stood proud, causing gasps of recognition. “The Great and Powerful Trixie!” the pony said theatrically. Indeed, Trixie stood, wearing the same cape and hat as when the Mane 6 had first met her.

“But why?” Twilight asked.

Trixie snorted, “You shamed me that day many months ago,” she said, “every town had heard of this and laughed as I came and left. I was alone and angry.”

“I met her,” Victorious added, “as I tried to grow accustomed to this new body and these new surroundings. I showed her what you show every companion you meet Doctor.” He held up a hoof and revealed a device around his wrist. The Doctor recognized it as a Vortex Manipulator. “Not as smooth as a TARDIS,” Victorious continued, “but just as effective. Trixie has been my faithful companion ever since.”

“But why?” Twilight asked, “What does she get from this?”

Trixie spoke up, “Revenge against you is one.”

Victorious smiled, “The second will be that her child will help me lead the new Time Lords to victory!”

“Wait!” Twilight said, “How would her kid help you?”

Victorious turned towards the Doctor, “Do you want to explain?”

“For any child to have any of the abilities of a Time Lord,” the Doctor explained, “it must be conceived on the TARDIS.”

Everyone was quiet as they connected those dots. “And who better,” Victorious said, putting a hoof around Trixie, “to father the future leader of the greatest species in the universe than me?”

The Doctor shook his head, “That is so wrong.”

“Is it as wrong as clouds never moving?” Victorious asked, moving away from Trixie, “Is it as wrong as having eight wives because one cannot give a son? The world is wrong, and we will correct it. Father and child, with mother immortalized in history books forever as the bringer of the dawn of a new era!”

“I will give you an choice:” the Doctor said, “Stop now and live in Equestria peacefully. Or I will stop you.”

Victorious stared coldly, “I am Victorious!” he said, “I don't need to make a choice because I never lose! I will bring the Time Lords back and we will rule the universe as we should have. This is my choice!”

“Then I'm sorry.” The Doctor said, “I'm so sorry.” A light shone from the machine and Victorious and Trixie both turned around. Twilight's Element was shining and the machine made strange beeps and whistles.

“What are you doing?” Victorious shouted as he ran to the machine, “There's too much energy, your melting the systems!” Twilight was focused, her eyes shut, as her magic flooded the machine.

“You never knew this,” the Doctor said, “all of these ponies are attached to their elements. Twilight's just using that link to her advantage!”

Victorious held up his screwdriver and fired a beam, but the beam sizzled out before it could hit Twilight. He pressed buttons on the controls, “Stop them!” he yelled to Trixie. Trixie turned but was then tripped by a lasso from Applejack, who then tied her up quickly. Victorious screamed in rage as the machine started to groan and beep. The other Elements each began to disappear one by one until Twilight's was left. Then Twilight teleported everyone to safety as the machine exploded.
*********************

Everyone appeared a few yards away from the cave, the smoke visible for miles. Victorious stood, his face oddly blank. “Victorious,” the Doctor said, “come with us back to Equestria and try to live a normal life like everypony else.”

“Like the rest of you?” Victorious said, “Like all you filthy simpletons? To forget my calling and live alongside a species that isn't mine? Doctor, you won this battle, but eternal victory will always be mine.” Then, faster than anyone realized, Victorious lifted his laser screwdriver to his head and pressed the button. The beam shot cleanly through and Victorious collapsed.

“NO!” the Doctor shouted as he ran towards Victorious. Trixie started crying, whether from love or defeat nopony knew. The Doctor looked over Victorious as everypony was quiet.

“H-he's like you right Doctor?” Fluttershy asked, choking, “He can regenerate. Right?”

The Doctor looked at her, “The death was instantaneous.” he said, “He died before he could have the chance.”

Fluttershy cried, no matter how mean or twisted, no one should have to die. The Doctor gathered fallen branches and placed them around Victorious. “What about Trixie?” Twilight asked.

“Let her go.” the Doctor said. As soon as the rope was off Trixie bolted for the forest and disappeared in the trees.

Twilight walked up to the Doctor, “What are you doing?” she asked.

“A Time Lord's body, even in Equestria, is a dangerous thing. It has to be burned.” He turned towards her, “Where are the Elements?”

“Back where they belong.” Twilight said, “Can I help?” The Doctor only nodded and soon everypony helped in covering the body until nothing was visible. The Doctor rubbed two sticks together to start a fire and threw them on the wood pile. As it lit brightly Twilight walked towards the Doctor.

“It's not his fault.” she said, “He was tortured for years and forgot about friendship and love. That can drive anypony mad.” she looked towards the fire, “He's at peace now.” The Doctor nodded and smiled slightly. Even though he tried to kill them, Twilight still felt remorse for him, as probably everypony did.

He looked at the ashes rising to the sky, “Ponies are such amazing creatures.” he whispered.