A hundred years have passed since the conclusion of the Mega Man X series. Following the defeat of the Mavericks in the Maverick Wars, humans and Reploids live harmoniously in the utopian Neo Arcadia. As energy sources begin to dwindle, the ruler of Neo Arcadia, Copy X, sets out to ruthlessly purge the world of Reploids, thereby reducing energy consumption. A young scientist named Ciel forms the Resistance alongside the remaining Reploids in an attempt to stop their own genocide. All seems lost, however, until the Resistance stumbles upon a legendary Maverick Hunter...