Here we are in the year 22XX…
After the legendary heroes of the Reploids, X and Zero, defeated Sigma a long time ago, a new army was formed to stop the spread of the Maverick Virus and put a stop to any further outbreaks of the disease. But as time went on, the army became oppressive and started meting out a brand of justice that was characterized by paranoia. It is said that their leader, who was once a great warrior, has turned cold and calculating and will eliminate any Reploid that has the audacity to oppose him.
In these perilous times, a hero is required, and Ciel and her band of rebels have found one in an old ruin: a hero from the past who has been reborn in the present.
Zero has traveled to a time that he is unfamiliar with in order to protect it from a figure from the past… the freedom of the world is dependent on his actions.