Acting as a prequel to Mega Man Maverick Hunter X, it follows Maverick Hunters led by Sigma to face a giant, rebellious mechalonoid. With X unwilling to hurt a hostage, Sigma takes the enemy on and berates X. Sigma later discusses X's potential for free will with Dr. Cain, something Sigma does not see power in. Meanwhile, X and Zero become suspicious about several maverick incidents occurring at the same time. It is revealed Sigma has hacked a massive maverick to distract the hunters as he frees several others including Vile. After disabling Zero, Sigma forces X to remove his weaponry and destroys Abel City, killing Dr. Cain in the process. X then remembers his early days in which Light, who was dying, told X how he gave him the power to develop his own mind and that he entrusts X to use power. X fights back, but only damages Sigma's head. Satisfied with this development, Sigma escapes to start his rebellion, leading to the game's beginning.

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