A man wakes up to find he's inhabiting the body of a cartoon horse who wasn't exactly Mister Popular, judging from how shocked the locals are when he says things like 'please' and 'thank you'.
After the end of their first life as ponies, Ganondorf, Link, and Zelda are reborn as the Cutie Mark Crusaders shortly before the return of Nightmare Moon. May the Golden Goddesses have mercy upon Equestria.
Having long grown utterly bored with the destiny the gods had decreed for him, Ganondorf decided to take matters into his own hands and escape to a new dimension where he could be free. Even if that would mean turning into a pastel colored pony.