The legendary heroes of the Reploids, X and Zero, defeated the evil Sigma long ago, and a new army was created to prevent outbreaks of the Maverick Virus. But as time went on, the army became oppressive, and began to deal out a paranoid brand of justice. It is said that their leader, once a great warrior, has become cold and calculating, eliminating any Reploid that dares oppose him.
A hero is needed in these dark times, and that is exactly what Ciel and her rebel group have found in an old ruin...a hero from the past, reborn in the future.
Zero has come into a time he does not know, to save it from a figure of the past...the fate of freedom rests on his shoulders.