Just because Sigma was defeated, doesn't mean the war is over!

Six months after Mega Man X's defeat of Sigma, the rebuilt Maverick Hunters, now led by X, are finally containing the last scattered pockets of Maverick resistance. Suddenly, as if from nowhere, eight new Maverick Commanders emerge to lead a resurgence in Maverick activity across the earth. As if things couldn't get worse a new organization, the X-Hunters, determined to kill Mega Man X and avenge their master Sigma, appear and challenge X. And they have the juiciest bait to force Mega Man X to fight them, the body parts of X's dead friend and mentor Zero.

Determined to prevent the desecration of his best friend, Mega Man X leaps into battle once more. But things aren't as they seem, and the ghosts of the past are never as easily forgotten as it might seem.