After years of war, the Earth is finally safe, but the hard-won peace is shaky at best. Mavericks continue to rise up and the Maverick Hunters, already strained by fighting, are dealt a serious blow when ace Hunter Mega Man X, tired of the constant violence, retires from active duty. Picking up the pace, independent Maverick hunting splinter cell factions and militias pop up, with a group known as "Red Alert" being the best of the best. Spear-headed by Red and a mysterious Reploid named Axl, who has the ability to morph into other Reploid forms relative to his own size, Red Alert stems the tide of Maverick activity. Yet over time their actions become more and more unpredictable and murderous. As a result Axl, with dreams of being a REAL Maverick Hunter and fed up with Red Alert's actions, goes rogue, leaves the group and makes contact with the Hunters. Red Alert retaliates and challenges the Maverick Hunters to a contest of sorts; if they win, the Hunters get Axl, but if Red Alert wins...
With nothing to lose, Zero, Axl and even X himself, take up Red Alert's challenge and enter the fight once again...