After recovering from engine failure two years prior, Mega Man Volnutt, Roll Caskett and Data continue their quest for the Mother Lode. Verner Von Bluecher, Professor Barrell's companion, has built an airship named "Sulphur-Bottom", which he claims is strong enough to penetrate the storm hovering over Forbidden Island (an unexplored island that they've attempted to explore before). However, while en route, a mysterious woman, disguised as a reporter, attempts to dissuade Von Bluecher, Barrell and all those on board to enter Forbidden Island. When she fails, she orders Gatz to fire at the Sulphur-Bottom, but what was supposed to be a warning shot severely damages the airship and it begins falling towards the island.

Mega Man and Roll, watching the entire event on TV, head towards Yosyonke City to ask for help and to learn more about Forbidden Island. After rescuing the Digger Joe from the Abandoned Mine in the outskirts of the city, they manage to borrow a dropship and set forth for Forbidden Island. After fighting numerous Reaverbots and witnessing various sights, the storm stops and the Sulphur-Bottom is rescued.

On board the Sulphur-Bottom, Von Bluecher and Barrell entrust Mega Man and Roll with the task of looking for and retrieving the Keys to the Mother Lode, lest they be found first by the Air Pirate Alliance who may use them for evil. Along the way they try to find out more the mysterious woman that resembles Roll's mother, Sera, the mysterious girl found on Forbidden Island, and Mega Man's forgotten past.