A pirate-woman named Ruby-Heart who united fifty-two of the Earth's strongest heroes and villains, transports them to another dimension on her enormous battleship to fight an evil shape-shifter named Abyss who wants to rule all realities.
Reploid scientist Dr. Doppler has cured the Mavericks and built the Utopian Dopple Town. But after the 'cured' Reploids go rogue and assault Hunter H.Q., Mega Man X takes Zero's aid and sets out to combat his new foes -- and finds old ones.
The RPD are investigating strange cannibalized corpses on the outskirts of the city. The Alpha squad, Jill and Chris, are sent to locate missing team members. While there mutated dogs cause them to flee into a supposedly abandoned mansion.