After The Storm King successfully conquered the lands and the cities of Equestria, he and his second-in-command Tempest Shadow gained all the magic of the alicorns with the Staff of Sacanas. Then Storm King discovers a new world full of rich resources he can utilize for his own tyrannical empire. Thus, he will not only rule one world but also two and much more. Batman must find a way to defeat him before the villain can accomplish his evil plan.

Note: This takes place during the events of My Little Pony: The Movie and after the events of Batman Beyond: Return of the Joker.