The Doctor awoke, on the ground of the TARDIS, he got up and took a good look at himself, "Okay, I'm a talking horse, with an hourglass tattoo on my flank, in a crashing TARDIS, being chased by a my arch enemies, I've honestly had worse days."

PonyVille Library
Twilight, awoke to a seemingly normal morning, Until she got a knock on the door, "I wonder who that is." she said, thinking about something more cliche than what she had just said. When she opened the door it was a strange pony who seemed to have an essence of insanity around her, Pinkie Pie (you thought it was the Doctor didn't you?)
"Good morning Twilight, how are you?" the pink pony asked.
"Oh I'm fine Pinkie how about you?" Twilight kindly asked.
"I'm great, in fact so great! There's a new Pony in town, and i'm throwing him a party tonight, are you going to be there?" Pinkie asked with a grin that would make anyone say yes.
"Of course, I mean in a town this small a new pony is something we rarely get, what this new pony's name anyway?" Twilight asked, with a curious tone.
"Oh, i don't know i just saw him and new he wasn't from around here, so if you see a brown colt with an hourglass cutie mark, tell him to be at Sugar Cube Corner at Seven." Pinkie said then bounced off.

A back alley in PonyVille
"Okay old girl, now that we have you stabilized, you can self repair while i go get used to my new body." The Doctor said to the TARDIS. He walked around surveying the town, all ponies like himself, the only thing out of the ordinary was a pink pony bouncing around telling everyone something about a party until she finally reached him.
"Hi there," the Pink pony said, "I'm Pinkie Pie, and i hope your ready for your party tonight at Sugar Cube Corner, seven o'clock sharp!" Pinkie said.
"Oh i'm afraid i'll be leaving by then, sorry." the Doctor said with a feeling of guilt.
Pinkie started putting the Doctor into a guilt trip, "But there will be Food and Cake, and Dancing-"
"Dancing," the Doctor interrupted, "oh I love a good dance, I'll be there, but then i must leave!" he insisted.
"Fair enough." Pinkie said.

Sugar Cube Corner
Twilight arrived with a small package, a book, her standard 'welcome to PonyVille' gift. She sat down with her friends and began discussing with Pinkie about the new stranger. 'who is he, whats he like, whats his name, is he staying long' all a bunch of questions resulting in an 'I don't know' from Pinkie Pie.

The Doctor arrived, everyone shouting "Welcome" and he shouting back "Thank you" and he made his fake introduction. "I am, Colt Swift, thank you for the party, and the gifts so let's get to it!"

As the night died down, Twilight got a chance to talk with the stranger "How are you enjoying PonyVille."
"Oh it's lovely but," he took out a tube with green bit on the end, which started to flash. "I really must leave as soon as possible-"

He was interrupted by another, strange colt entering, wearing a sharp suit. "Hello, I'm looking for one Doctor. Has anyone seen a brown colt with an hourglass on his flank."
"A friend of yours?" Twilight asked.
"Yeah you could say that, or you could say he's trying to kill me."

Twilight heard this and sprang into action, "You won't heart our friend!" she said.
"Oh, he's made a friend. You'll do just fine." he said, and grabbed her. "Doctor, if you want her back alive you'll meet me in the town square in one hour." and the two were gone.
"Twilight," Rainbow Dash said, " when we find that guy i'm gonna kick his-"
"No need," Interrupted the Doctor.
"Colt," Rarity said, "Do you know this doctor that strange stallion was referring to?"
"My name isn't actually Colt Swift," the Doctor explained. "I'm the Doctor and i'm going to save Twilight."
"Who was that Colt anyway," Applejack asked. "He seemed to know you just fine 'Doctor'." she said putting air quotes around his name.
"He's like me, a traveler with no name, so he took to calling himself the Master." The Doctor had a sad look in his eye.

The Town square
"When he gets here i will make him pay!" the Master said to no one in particular.
"Is that anyway to greet an old friend, Master?" the Doctor arrived. "Ms. Sparkle he hasn't hurt you has he?"
"No i'm fine, he's just been ranting about this Doctor. " Twilight responded.
"Well speak of the devil and he shall appear, wont he Doctor?" The Master screamed at his enemy's name.
"You, your the Doctor?" Twilight questioned.
"The thing about devils, is that they run when a good man goes to war." the Doctor replied, "I think you'll find that I am not going to let you win. And if you think that its a good idea, kidnapping innocent ponies to get to me," He was shouting, "then you've forgotten, you've forgotten every dark day in history, you've forgotten every one of our encounters, you've forgotten what i did for our people in the time war,you've forgotten what i did to our people, and you've also forgotten the most important thing about me."
"And what is that," the Master shouted.
"I'm not done regenerating." The Doctor smiled as he was surrounded by a golden light, which then seemed to attack the master. "I gave you, enough chances. Now i'm going to tell you, there is one thing that you will always remember, even after your gone. I am the Doctor, the Last of the TimeLords, and you are a memory that's been following me for too long."
The master was gone, not dead, just gone. The Doctor helped Twilight down from where the Master had tied up, and as her friends swarmed around her, he walked away. Returning to the TARDIS.
"Well old girl," the Doctor said. "I've faced my demons, we can go now."
As he was preparing to leave he was suddenly interrupted by six ponies and a baby dragon knocking on the TARDIS doors.
"What's this then," Twilight asked. "You still need to explain what just happened."
"Oh well, that was just a terrible figment of my imagination brought back to life during my regeneration, i absorbed him again, he's gone." The Doctor explained.
"So now your just going to hide in this box?" Rainbow Dash asked. "Some super hero you are."
This got to the Doctor, "would you like to step inside for a sec?"
As the seven entered they, where astounded. "I'ts bigger on the Inside, I know," the Doctor said, but as he tried to tell them to leave, the TARDIS sparked to life, and took them all far away from the dark alley.

Next Chapter: The Rainbow Dash episode in which she and the Doctor have a quarrel which results in them becoming closer as friends Estimated time remaining: 53 Minutes