The TARDIS.

"Okay, i guess your coming with me," the Doctor said. "GERONIMO!"
The TARDIS was doing its traditional spinning and flailing about in the time vortex, getting struck by lighting, and ultimately causing most first time time travelers sick, until it finally landed making its trademark noise.

"What in Celestia's name was that all about?" Rainbow Dash asked, "you pony-napped us!"
"I did no such thing," the Doctor replied. "The TARDIS did it all that when it picked up life forces."

Twilight finally got up, she looked around and said "What exactly is a TARDIS, Doctor? I've never seen any magic like it."
"Well you see Twilight, i'ts a Time And Relative Dimension IN SPACE, developed by my people so that we could see the universe." He explained, sounding quite proud.
"Big deal," Rainbow Dash said, "I can fly smoother than this hunk of junk."
"Oh, yeah?" the Doctor questioned, "go look out that door, right now, I dare you." He was getting furious at the pegasus.

Rainbow Dash accepted the dare, her jaw dropped when she saw that they where floating in space. Soon, everypony was having the same reaction as Rainbow Dash. then Twilight remembered to a few seconds ago, 'his people?' she thought, and decided to question him on the subject.
"What did you mean when you said 'your people' you look like any ordinary colt to us." she asked.
"Well since your all here, I suppose I could tell you. I'm from a different planet, I'm a different species entirely, I suppose a 'TimeColt' would be proper, from 'Gallopfrey'" he laughed to himself, not realizing the shock his new companions were in, "Oh come on, beginnings are so slow, let's get to the action!" The Doctor turned to the console of the TARDIS, "Oh here we go, the year is 3026, and we are orbiting the Celestia Colony ship 224." He told the others.

"Wait did you say year 3026, no that's impossible ," Twilight said. "The year is 1001, you must be wrong."
"Oh did I forget to mention, it travels in time?" he stuck his tongue out at Rainbow Dash, who muttered something under her breath. As the others were getting over their new surrounding, the Doctor went to a radio, "Celestia224, this is the TARDIS, permission to come aboard," he said rather formally. after a few seconds of white noise the radio sparked to life.

"Permission granted, docking bay 36 is your stop." the voice said.
As the TARDIS made a smooth landing everypony piled out of the TARDIS.

"Okay," the Doctor began. "I've never had this many companions so i want teams of two. We can meet back here in three hours." He tapped his wrist.

Everypony saw what a bad mood Rainbow Dash was in, so they all teamed up until it was only her and the Doctor. 'Great' he thought, 'I get paired up with her.'

They traveled the ship in silence for a good twenty minutes until Rainbow Dash finally spoke. "Why did you bring us here its boring!"
"Boring?" he said, "these are your descendants, traveling space and you think its boring?" he looked around and found that she was right. "I didn't bring us here, anyway the TARDIS did."

"Have you considered trading that one in for a new one?" she asked.
"There are no more, that's the last one and she's perfectly fine." the Doctor responded.

"For an advanced alien race, your kind of dumb." She stated. "And what kind of name is 'Doctor' anyway?"
"Its a fine name," he said. "and how would you know, I'm the only alien you've met."
"Well what about that 'Master' guy, he was the same as you wasn't he?" She said in an insulting way.
"Listen here missy-" he was interrupted.
"Missy? Your not much older than me, what are you like twenty." She mocked.
"Add about 900 years," he said, with a monotone voice.

Meanwhile, Fluttershy and Rarity where at some sort of food court. "So Fluttershy, what do you think of this Doctor?" the unicorn asked.

"Well-um, not to be rude, or anything but he seems... well older than he looks," the quiet pegasus replied.
"Well," Rarity thought for a moment, "He seems to fear nothing, as though he's seen it all, truthfully i'm envious."
As if the universe had a sense of irony, the alarm sounded, and ponies of all ages started shouting and running away from the noise, the captain cam on to the P.A. system. "Prepare for boarding, we are under attack by Dalek forces.

The Doctor heard the announcement and stopped everything he was doing. "Rainbow Dash i need you to find your friends, and get them back to the TARDIS, NOW!" He shouted. and she flew as fast as she could.

The Doctor ran to where the ship could be seen, it was definitely Dalek.

Back at the TARDIS

Rainbow Dash had gathered her friends, one by one they piled into the TARDIS.
"Where's the Doctor?" Pinkie had asked Rainbow Dash, who was about to answer until the TARDIS monitoring functions came up. they could see the Doctor, standing alone in a large hallway, when he was suddenly joined by three, horrible looking machines.

"DANGER DANGER, THE DOCTOR WITHIN SIGHT, EXTERMINATE, EXTERMINATE" the Machine on the left said.
"Yes yes, we've been over this quite a few times, but how about this time we skip it." The Doctor was acting differently than any if the seven friends had seen.

"Is he, angry?" Spike had asked, "Not like earlier with Rainbow Dash, he seems like he's a whole different pony."
"Shucks," AppleJack had said. "He looks madder than a hare at a tea party."

"Pfft, whatever," Rainbow Dash said. "He's just got to kick over a couple of trash cans, why is anyone concerned?" she said, secretly worried about him.
They looked back to the screen, "WHAT IS THE PURPOSE OF YOUR BEING HERE" one of the machines asked.
"Well it was to have some fun, but it looks like I'm going to have to stop you, aren't I?" The Doctor said. "Now i want you to scan through your data core, and think of the words that the ancient Daleks refer to when they speak to me."
The Dalek hummed for a second, then spoke "MERCY!"
"What am I?" the Doctor demanded.
"MERCY, MERCY!" the creature pleaded.
"What AM I?," he raised his voice.
"THE LAST OF THE TIMELORDS." The Dalek responded.
"WHAT AM I!" the Doctor shouted.
"THE ON-COMING STORM, DESTROYER OF WORLDS!" The Dalek spoke.
The Doctor spoke one word, "Run."

The Daleks teleported back to their ship and immediately fled.

The TARDIS, orbiting Celestia224.

While the others were talking and laughing, the Doctor was looking out into the void of space, when Rainbow Dash sat next to him. "Let me guess, i needed to beat the Daleks in a way that was twenty percent cooler." He joked.
Rainbow dash looked at him, "Why did they call you the last, of the TimeLords?"
"I've made a lot of mistakes in my life, I've ruined a lot of lives. I am the last, and they fear me because I killed the others." He said.
"Why would you do that?" she asked him.
"we were losing a war, we had a backup plan, it would've killed all other life in the universe." he said, "so instead i wiped out my people and the Daleks." The Doctor noticed that the background noise had ceased and turned around, everypony was listening to his story. "Well I'll be getting you lot back now, after all I did say i would take you back didn't Rainbow Dash?" he asked.
"You know that was when i thought you where some crazy colt with a box, so i guess we can keep going." she replied. Everpony cheered and before he went to the console, he pulled Rainbow Dash aside. "I am a crazy colt with a box." He said.
"Doesn't take a time traveler to figure that one out," She smiled at him.

Next Chapter: Don't let me slow down. Estimated time remaining: 47 Minutes