Dr. Light has created a super-intelligent robot named Brain Bot. Brain Bot has a knack for tinkering with things, inspecting them and repairing them even though there is nothing wrong in the first place. Unfortunately for Mega Man, Roll and Rush, they have to personally transport him to California. Even worse news is that Dr. Wily's satellite picks them up on their way. Mega Man is successfully able to repel Wily's robots, but Brain Bot gets captured anyway. Now Mega Man has to rescue his new incredibly intelligent (but painfully annoying) friend from Dr. Wily before the madman is able to use Brain Bot's own cyber brain for his own evil purposes.