After suffering his previous defeats to Mega Man, Dr. Wily turns up at Dr. Light's laboratory, having apparently undergone a change of heart. Dr. Light takes him in, and the two begin work on Gamma, a great robot intended to maintain the world's peace. Near the end of their work, the two need energy elements from eight unknown planets to activate Gamma.

Suddenly, though, Wily's Robot Masters in charge of mining and processing the elements on those planets begin to go berserk. Mega Man takes off to quell the robot rebellions and investigate their cause, but new mysteries await him as well.