The game begins with Mega Man Volnutt exploring a tower ruin in the middle of the ocean, where he retrieves a large blue refractor. After defeating the Reaverbots guarding his path, he returns to the airship, the Flutter, and departs from the ruin. However, the Flutter suffers from engine issues and crash-lands on Kattelox Island. Stranded, Mega Man, Roll, and Barrel begin searching for parts to repair the airship.

While on the island, pirates led by the Bonne family attack Kattelox City, using giant mechanical weapons in their hunt for the island's legendary treasure. Mega Man decides to intervene and protect the city. He defeats the pirates' forces, including Tron Bonne and her robots in the Downtown area, and Bon Bonne, who leads the siege on City Hall. Afterward, their leader Teisel Bonne plans an assault on the Clozer Woods ruins, but Mega Man also defeats him, safeguarding the island.

The island's mayor, Amelia, reveals to Mega Man that the Bonne family is searching for Kattelox's secret treasure. Legends claim that uncovering it would bring about a great disaster for the island. Concerned about strange activity in the island's ruins, Amelia asks Mega Man to explore them and investigate the increased presence of Reaverbots.