In Mega Man Zero, Mega Man awakes after 100 years of sleep to a world where reploids 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 punished for trifling suspicions. Reploids, who have managed to escape from the punishment, flee to an old city which now lies in ruin, but the evil Neo Arcadia's hands are advancing. A genius scientist named Ciel, who lives with the innocent reploids in hopes of saving them, tries to revive the legendary reploid Zero in order to save the cornered reploids. As the hero Zero, it is up to you to save the world.