The Reploid War, sparked by the Sigma Virus that turned Reploids into mavericks lasted for centuries. MegaMan X put an end to the everlasting battle. At last, people were able to begin recontructing the world. The city of Neo Arcadia was established as a primary base for building a peaceful world. However, the "peace" people were creating became a disaster for reploids. The goverment was fearful that the reploids would go berserk, so they accused and arrested them for any reason, or even for no reason at all! The reploids who were able to escape took refuge with Ciel, a former reploid researcher, in a abandoned city.

A researcher named Ciel wanders into an abandoned laboratory searching for a legendary reploid... Zero.