WEOORP WEOO W- What The Hell? The Doctor Exclaimed while typing away on the console keyboard. The TARDIS had stopped making any sort of noise including the usual background noise. He finally got a response out of the machine saying in Galifrieyan text that "ALERT ALERT System Capacity down to 25% Emergency Materialization Activated" after that went off the screen the power on the TARDIS cut and The Doctor could hear small explosions coming from outside the door of the machine.
Little to the Time Lords knowledge his tinkering around in the Charmelon Circuit to see IF he could make it work in case of Emergency caused the TARDIS to latch on to a small crack in the fabric of the Time Vortex sucking it in.
The TARDIS finally came out of the crack above a Small Town unbeknownst to the Doctor it was Ponyville.
Inside the TARDIS the Doctor was being thrown around like a Hackey Sack, He was bouncing off the walls as the Machine fell and eventually the Rate of Speed the Atmosphere of Equestria produced caused the TARDIS to catch on fire. As the TARDIS Crashed into the Ponyville Library the Doctor was thrown into the Console scream like a banshee and he cracked his head causing his scull to crack. He instantly passed out from the shock and the last thing he saw was his burning time machine and the door being opened.
The Doctor woke up in a Hospital bed, His skull wrapped in a cloth and a Ventilator shoved down his throat. Also there was some.... creature sitting in a chair a little bit away snoring away. He began to try assess his surroundings and injuries. The most he could gather was that he was in a Critical Care Ward in some alien hospital in another universe and he was getting treatments they would receive Not Timelord Treatments and whatever they were doing to him was causing his Central Nervous System to shutdown. He realized the only options were to either A: Die a painful death in a Hospital or B: Regenerate, Find his TARDIS and Figure out What the bloody hell happened. He obviously chose B. He began the painful process
of Regeneration which woke up the sleeping creature who said "Oh your a awake after 12 hours my name is Twi-..." She then noticed that the thing in the bed was glowing a orange out of it's hands "What are you doing" She said. The Doctor said through gritted teeth "Look..... Away....." as soon as he said that his body exploded into the orange Regeneration
Energy which caused all the medical equipment attached to him to dissolve. All the nurses reached the room just as the process was ending and where the unknown being was a Brown Pony with Spiky hair was in it's place. "Hello" The Doctor said completely unaware of the fact he no longer was human until he looked down at his hooves. "Oh Crap"