Several months after the Repliforce war, Earth is at a peaceful time. The repair of the space colonies damaged during the war was almost complete, the only space colony remaining being the giant colony Eurasia located in a Lagrangian point. As it was quite old, it was planned to receive extensive renovation. However, one day someone had occupied Eurasia and took control of it, scattering a virus in the colony and using its artificial gravity systems to set it on a collision course towards Earth. Within 16 hours, Eurasia will crash and cause great destruction, in the worst case extinguishing all life from the planet. The Maverick Hunters plan on using the large particle cannon Enigma to destroy Eurasia before it happens. The Enigma cannon is somewhat old and needs to be upgraded. Signas, the Hunter's new commander, orders to Mega Man X and his comrade Zero, as they race against time to collect the four parts necessary to upgrade the Enigma and stop Eurasia before it's too late. To make things worse, Sigma scattered the Sigma Virus all over the world and the parts needed are being protected by Mavericks.