After discovering a virus that is turning intelligent and peaceful robots known as Reploids into rogue Mavericks, the scientist Dr. Doppler successfully creates an antivirus to the phenomenon. The reformed Reploids then move into Dopple Town, a place where humans and Reploids can live together in harmony. But when an outbreak occurs causing the Reploids to turn back into Mavericks, Maverick Hunters Mega Man X and Zero are sent to contain the situation.

Choose either Mega Man X or Zero as you run, jump, dash, scale walls, avoid obstacles, and fight enemies in eight challenging stages. At the end of each stage, defeat the boss to gain a special weapon that will aid you in the upcoming battles. Will you be the cure for this latest outbreak?