The Doctor has found himself stranded in Equestria. A way back will take time. A lot of time. During the interim, he needs to blend in, so he uses the chameleon arch to turn himself into a pony, complete with a (mostly) pony mind. To a large degree, this will be the story of an out-of-place stallion trying to settle into Ponyville (with the possibility of some adventuring in the future). Of course, nothing's ever easy for The Doctor.
This is good, I'm hoping for an epic doctor reveal at the end, Don't let me down!
This still interests me, please keep it up.