The Doctor and Derpy have lost each other in a confrontation against interdimentional beings bent on conquering the Equestia Universe. The struggle sent the beings back to where they came from, but also leaving Derpy in an alternate reality.
Doctor: Being a Time Lord the Doctor has had to raise barriers between worlds to keep the threats in a new-found void. Oh well could have been worse. Derpy could have accidentally ended up in the Doctor's universe.
Derpy: Now trapped in this new Equestria Derpy must learn to adjust. After living there a while she has found out that some of the ponies talk to floating words. Luckily with her right lazy eye she can see her world. Some kind of wibbly thing.
I figured I'd do a Doctor Whooves parody of the infamous scene in Doctor Who season 2 finale Doomsday.