Mega Man is a robot created by a brilliant scientist named Dr. Light, who hoped many his many creations would only be used for good. One day however, a mad scientist named Dr. Wily stole Light's original 6 robots and creation plans. From them he began creating a whole new series of robots, with one goal... World Domination! But Dr. Light gave Mega Man the ultimate trump card when he built him. Mega Man possesses the ability to absorb the powers of other robots. Now Mega Man and his best friend, a robotic dog named Rush fight for everlasting peace against the evil Dr. Wily!
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An underwater mining operation falls under attack by Dr. Wily, who traps Dr. Light and Mega Man in a small prison.
Dr. Wily intends to use his new shrink ray on several cities, but his Robot Masters turn it on Mega Man.
Dr. Wily has built a teleporter, which doubles as a body switcher, resulting in Mega Man and Snake Man trading bodies.
Dr. Wily gets his hands on some super freeze technology, which he hopes will force city leaders to leave. But Ice Man gets the feeling Air Man is replacing him and switches sides.
Dr. Wily's robots disguise themselves like a rock band to unleash a mind controlling music. Only Mega Man, Roll and a young deaf girl remain unaffected.
Dr. Light's time machine sends Mega Man to a future where Dr. Wily controls the planet. Mega Man must find a way home and save this future.