It's a disaster! Doctor Light's lab has been attacked by Doctor Wily, and stolen some crucial parts for robots. And, if it weren't bad enough already, he has taken Roll as a hostage! Mega Man and Proto Man go to stop Wily and stumble upon Duo, the big alien robot, who is willing to help. And Bass, still angry that Wily has revived more Robot Masters, again teams up with the good side to destroy the enemies...