The story begins three weeks after Mega Man X5, with Zero missing, presumed dead, and the Earth's surface rendered uninhabitable. Rumors are spreading through the Reploid World of a Maverick named the Zero Nightmare, a Reploid of pure evil that is spreading chaos throughout the world. X, curious about this Maverick, and angered by its use of his late friend?s name, seeks him out.
After destroying the Zero Nightmare, X learns that Zero is alive, just recovering from damage sustained in the last game. When Zero is recovered, he joins X and they seek out the researchers who built the Zero Nightmare.
X finds the lead researcher, Gate, in his lab. After X defeats Gate in battle, Gate reveals that he has rebuilt Sigma, the leader of the Mavericks. Sigma kills Gate, then challenges X to a duel. X is able to defeat the rebuilt Sigma.