Dr. Wily is at it again! This time he's uncovered an ancient temple that houses a super computer he uses to recreate some of his old robots (from Rockman 2 and Rockman 3). Another added effect of this computer is that it can affect anything electrical, which he of course uses to his advantage. Rockman's sister, Roll, is one of the first to get affected by it. Dr. Light manages to make Rock and his friends (the robots from the first Rockman) immune to the evil computer and they set off to stop Dr. Wily once again on the island where he's hiding.

The game plays out like an interactive anime mini-series where each disc in the game is an "episode" with opening and ending credits. The player basically follows the plot through numerous movie clips and every now and then is asked to make decisions, be it a reply to a character, the left or right path, or even some quick time events. Aside from this the player is also thrown into battles at certain key points of the game, where the game switches to a static first person view in which the player has to kill whatever enemy or boss has crossed Rockman's path.

In true Rockman fashion, Rock absorbs the powers of any boss he defeats along the way, to be used against another boss later on in the game or any difficult enemies he encounters.