Just when Mega Man X thought he had brought down all the X-Hunters, several months later an uprising moves from within an abandoned factory. While 8 all-new X-Hunters occupy Mega Man X, a triple threat plots to resurrect a secret weapon that is all too familiar!

The good Dr. Light supplies Mega man X with incredible new abilities hidden in capsules buried deep below the surface. And with new vehicles like the mobile attack cycle plus powers he gains from the X-Hunters, Mega Man X will be ready to face his destiny as a Maverick Hunter. Now it's all or Zero for Mega Man X!

Six months after the rebellion of Sigma, the most powerful repliloid in history. The number of irregulars, which had once seemed to have decreased, continued to increase, and irregular hunter bases were being destroyed in various locations. The irregulars that were causing these incidents had special control chips implanted in them, and the "Σ" mark, which was supposed to have been destroyed, was engraved on the chips.