After getting knocked out in battle, Mega Man has a dream flashing back to when he was first created by Doctor Light and how he reprogrammed him into the Blue Bomber he is today.
Dr. Wily takes over the power grid with a device that allows him to control machines through electricity. He then proceeds to attempt to take over the city with soda machines and monorail cars and only Mega Man can stop his plans.
A devolution acid that effects robots is raining in Robosaro Park, Dr. Wily's robots aren't effected by it because he had them vaccinated and Dr. Light must find an antidote to stop it from happening.
Dr. Wily attacks an underwater mining operation, then tries to get rid of Dr. Light and Mega Man with a fake laboratory that turns out to be a mobile prison.
Dr. Wily steals a super freeze technology to create a giant glacier and freeze cities, drive out their leaders, and replace them with his robots. Ice Man, however, decides he's being replaced by Air Man and double-crosses Dr. Wily.
A new hit song by the band, Cold Steel, is causing people all over the world to get hypnotized. Little do they know, the band is Wily's robots in disguise.
Mega Man is accidentally booted to the future by a time machine, where he discovers that the evil scientist Dr. Wily has taken over the planet. Mega Man must find his way back to his own time so that he can reverse this horrible future.
