In Mega Man Zero our hero awakens after 100 years of sleep to a world where innocent reploids (robots) are unjustly attacked by an organization called "Neo Arcadia". This new government has turned the world into a place where it is extremely hard for reploids to live and where they are under constant persecution. Reploids who have managed to escape from the punishment flee to an old city which now lies in ruin, but the evil Neo Arcadia is closing-in on their location. A genius scientist named Ciel, who lives with the innocent reploids in hopes of saving them, tries to revive the legendary reploid Mega Man Zero in order to save the cornered reploids. As Mega Man Zero, it is up to you to save the world.