In the aftermath of Mega Man X8 and Lumine's defeat, Axl lies in a coma and X feels powerless in the face of his teammate's condition. Zero urges him forward: there is no time to mourn. Years pass. Then strange events begin unfolding at the old Jakob Project building, and a pulse of energy begins radiating outward from Abel City, causing its structure to collapse. Waves of Mavericks rise from the chaos. Before X and Zero can respond, a clone of Zero attacks the Maverick Hunters' base — an impossibility they cannot yet explain. They fight through it and head to the city, only to discover that the old Jakob tower is the source of the catastrophe, reanimating defeated enemies to destroy everything in range. X and Zero must stop the invasion before the city falls and the disaster spreads across the planet.