Set 10 years after the Akatsuki destroyed Equestria, the new Akatsuki return after a fatal event in Konoha.

Their old comrades have divided the land amongst themselves, and sent the remaining ponies in exile across the land.

With few allies and resources, the Akatsuki must fend off the ponies' counterattack, hide from their own world, and stay alive to prevent the collapse of the Akatsuki.