Cia has used the complete Triforce to break apart time and space for her selfish purposes, branching off the timelines of Hyrule into easy to access dimensions. And now Link, along with the Warriors of Hyrule, must branch off into these worlds, but this is not their tale.

Meanwhile, the magic leaks off into Equestria and Canterlot High thanks to residue energy from high magical activies in those worlds. Not only that, but the heroes of two separate timelines wound up there as well: The young Hero of Time and the cartoony Hero of Winds.