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.
Our hero finds herself in a strange world, and in a strange new form. Maybe this could be a fresh start, you ask? The thing is that she wasn't aware she needed one.
An accident with the Mirror Portal ends up with Twilight stuck as a small pony in the Equestra Girls' world. Her friends can't get over how cute she is.