This is set before Doctor Whooves met Derpy. And thanks to Hasbro my Derpy is also now OOC.
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The TARDIS shook as it flew through the time vortex. The Doctor rushed about attempting to fix the problem. He took a quick look at the scanner.
"Fourth Wall." He said going back to his work. He suddenly did a double take. "Wait... fourth wall?" His eyes widened as sparks flew from the console. He rushed about trying to get to a different place. The TARDIS wouldn't be able to withstand the force of breaking through the fourth wall. This was bad. Really bad. There was a sudden flash and a loud bang. Then...everything went dark.

The Doctor's eyes flickered open. He stood up and looked around the TARDIS. It was dead. Not only that but... it looked like a cartoon. The door slammed open and there stood a grey pegasus with eyes that went two seperate ways. The Doctor stared. The pegasus looked at him angrily.
"WHAT DO YOU THINK YOU'RE DOING CRASHING YOUR BOX ON TOP OF MY HOUSE!?" She roared. The Doctor was taken aback.
"You could have asked if I was okay." He said, standing up. The pegasus just scowled.
"Why don't you just move your box?" She asked. The Doctor flipped a lever. Nothing. He looked at the mare as if to say 'see?' The mare turned round and walked out of the TARDIS. The Doctor sighed and stood still. He was trapped. And he had no idea where he was.

Derpy sat on a lone cloud. Why did that man crash his box onto her house? More importantly, what was that box? It all seemed so familiar. Like something she used to watch when she was younger. A show called... Doctor Whooves. Her eyes widened. She sped towards the ruins of her house. She was confused. But she was certain this was him. She landed infront of the blue police box known, in the show, as the TARDIS. She pushed open the door. The pony looked up rapidly and stared at her.
"I know who you are." She said. The Doctor's eyes widened.
"How do you know?" Then he realised "Oh." Derpy smiled. A scream came from outside. The Doctor rushed to open the door. They both ran outside and stared at the sky. A fleet of saucers hovered in the sky above Ponyville casting darkness across the village. Ponies rushed inside locking the doors behind them.
"What is that?" Asked Derpy, worried. The Doctor didn't answer he hastily ushered Derpy inside the TARDIS.

Derpy suddenly realised what they were. She was even more worried now. If they were in Ponyville everypony was in danger. The Doctor sighed.
"How did I even get here?" He mumbled into his hooves. It was his fault. If he had paid attention he could have stopped the TARDIS from crashing here. He stood up and peeked out of the door. The saucers were still there, as he had thought. He had to think of a plan. Derpy, meanwhile, was sat wondering 'why did I get myself into this?' The Doctor walked up to her. She looked up.
"You're going to have to trust me. Do you understand?" He asked. Derpy nodded. "These things are called--"
"Daleks." Cut in Derpy.
"Yes...wait. How did you know tha-- oh." Derpy smiled weakly. "When I say we run out of the TARDIS to the nearest place to hide." The Doctor explained. "Got it?"
"Yep." Replied Derpy.

"RUUUUUN!" Shouted The Doctor as the saucer fired another shot.
"HOW DID YOU GET ME INTO THIS!?" Yelled Derpy.
"JUST KEEP RUNNING!" A shot slammed into the ground centimetres from Derpy's leg.
"AGH!" They both dived as a Dalek flew out of nowhere and fired a shot the went just over The Doctors head. The shot hit a stack of nearby newspapers sending bits of paper flying. The Doctor and Derpy hid underneath the stall. The paper had been enough to distract the Dalek so they could jump.
"Target lost!" Exclaimed the Dalek in a robotic voice as it flew back up to its fleet. The two ponies sighed as they snuck out from their hiding place.
"What's your name, then?" The Doctor asked.
"Derpy Hooves."
"Nice to meet you, Derpy Hooves." The Doctor replied shaking her hoof. "Wait...I have hooves?"
"Well, duh! You are a pony!" The Doctors eyes widened.
"A-a-a what?"
"A pony! You even have a cutie mark!" Derpy replied pointing to his flank. The Doctor looked and sure enough there was an hourglass there.

The Doctor rummaged around. He had to find something. Anything that could help him stop the Daleks. Derpy watched as he threw items over his shoulder. He sighed and sat on his haunches. That's when he noticed it. A small glint out of the corner of his eye. He turned to look.
"Oh." He laughed "That's brilliant!"

The machine whirred as The Doctor worked. Derpy watched as he rushed about.
"Are you sure it will work?" She asked.
"100 percent sure! That it might not work." He replied, going back to his work. The machine lit up and the middle started spinning. The Doctor smiled and hastily placed it on the floor. He watched in satisfaction as a beam of light shot out of the top.
"Does this mean it works then?" Asked Derpy.
"Only one way to find out..." Replied The Doctor happily. "GERONIMOOOOO!" He dived into the beam and dissapeared as if he were being sucked into the machine. Derpy gasped as a spark flew from the machine and the beam shut off. If it had worked...he was trapped on the ship.

The Doctor landed on the floor with a /thump! The Daleks turned to look at the intruder. Many of them backed away while three stayed still. The Doctors eyes widened when he saw them. They were meant to be dead.
"Dalek Sec, Dalek Caan and Dalek Thay." The Doctor said, worried. "Why attack this place?" He asked.
"They are enemies of the Daleks!" Exclaimed Dalek Sec.
"In what way?" Those three words left The Cult of Skaro speechless. "You better be careful what you do. Because I am not in the mood for you three." Dalek Sec was the only one brave enough to go right up to The Doctor and ask the question.
"And how will you stop us?" The Doctor looked at him fiercely.
"You either leave or I blow your fleet out of the sky." He replied, angrily. Dalek Sec backed off slightly. "Your choice." Every eyestalk was on him as he stood there. None of the Daleks answered. "5." The Daleks were getting uncomfortable. "4." They started looking around but they still didn't move. "3." Nothing. "2." Still nothing. "1." The Doctor got out his sonic screwdriver and soniced the control panel. A siren sounded and a bright red light filled the room.
"All systems are down!" Exclaimed Dalek Thay.
"Have fun with that." The Doctor said turning to go. The teleport had gone off. "Oh, what the b---!" The huge saucer crashed into the ground and the others took off into the sky.

Derpy rushed out of the door of the TARDIS after hearing the crash. She stared at the wreckage. He was dead. Out of the corner of her eye she saw a small glow. She never thought to look. Until it started to grow brighter. She turned just as there was a blast. The rubble was blasted aside as The Doctor lie there a streaming yellow glow flowing from his face. His mane and face was changing. Soon it stopped. The Doctor stood up.
"Hello." He exclaimed. Not only had his appearence changed but his voice had as well.
"H-h-hello." Derpy stammered. She had seen the real doctor regenerate. She smiled and laughed.

"So. Guess this is goodbye then." Said Derpy.
"Actually." The Doctor said "How would you like to travel with me?" Derpys eyes widened.
"T-t-travel with you!" The Doctor smiled.
"Yep."
"Y-y-yes!" Derpy exclaimed happily. She was going to travel with The Doctor! She had always wanted to travel with him and now she could! The Doctor smiled. The TARDIS had fixed itself over time as it did.
"Come on then!" He exclaimed "We've got adventures to go on!" They walked inside smiling. There was a woosh as the TARDIS began taking off.