The Reploid war, sparked by the Sigma Virus that drove reploids beserk, lasted for centuries. Finally our hero, Megaman X, put an end to the ever lasting battle. At last people were able to begin reconstructing the world.

The city of Neo Arcadia was established as a primary base for building a world where everyone could live happily. People went at the restoration work chearfully, with smiles on their faces. However, this "people's paradise" soon became a disasterfor repliods. The goverment, fearful of the threat of repliods going beserk,accused and arrested them for any reason - or no reason at all!

Those forunate reploids who could escape where forced to seek safety in a devastated city. To stay alive, they mined its limited stores of energy for their own use,Ciel, a human and former reploid researcher, emigrated with teh reploids to the ruined city. She could not abandon them while they were falsly accused by the goverment. She was determined to find away to help them.

The evil hand of the government is about to extend to teh reploid sancuary. The reploids will all die if something isn't done quickly. Ciel remembers teh name of Zero, the legendary reploid rumored to be sleeping in suspended animation at some hidden place near Neo Arcadia.

"If the legend is true ... he might save uss..."