Much later after the fall of Dr. Doppler and Sigma, a large civilization of reploids has developed. This mass of reploids is called the Repliforce. The Repliforce is a peace group of Reploids that see themselves as citizens of the world and do not take kindly to Mavericks. This makes things good for X and Zero, that is, until the Repliforce starts to have problems. Sigma organizes an attack to frame the Repliforce into being accused as Mavericks. In protest to the human accusations, the Repliforce begins a coop against the humans. X and Zero are then sent into action to try to reason with the general and the colonial of the Repliforce and get them to stop the coop. Needless to say, the colonial and the general don't want to hear it. They continue the coop... causing X and Zero to fight again.
The whole time this is happening Zero is suffering from dreams about his origin. In the dreams he sees a man with a mustache and frizzy hair. The man also talks with a German accent (Any Mega Man fan will know how this person is Wily, but for the sake of the story, we don't know). Zero isn't sure who this man is, but as he fights Sigma he hopes to learn more about his past and his purpose.