On a tower ruin in the middle of the ocean, Mega Man retrieves a sizable blue refractor. Defeating the Reaverbots blocking his way out, he makes his way to the Flutter, which leaves the ruin. However, the Flutter experiences some engine problems and crashlands on Kattelox Island. From there, the Casketts try to find a way to repair their ship. However, when pirates attack Kattelox's city with giant mechanical weapons, Mega Man decides to stop them. Mega Man defeats the armored robots patrolling Downtown, led by Tron Bonne, and the ones laying a siege to City Hall, led by Bon Bonne. Their leader, Teisel, decides to attack the Clozer Woods ruins, but Mega Man defeats him as well. Kattelox's mayor, Amelia, tells Mega Man the Bonnes are searching for the island's secret treasure and that legend says if somebody obtains it, a great disaster will befall the island. Amelia asks Mega Man to investigate the island's ruins. In the Forest Ruins, Mega Man finds a large yellow Refractor. He uses this to power a boat in Uptown to access the Lake Ruins, defeating the Bonnes who had stolen the other boats and turned them into robotic weapons. Mega Man finds a huge red refractor in the Lake Ruins, which Roll and he use to repair the Flutter to access the entrance to the Clozer Woods ruins. Inside, Mega Man unlocks the island's largest ruin, the Main Gate, hoping to find the reason why Reaverbots from the island are being activated. On the way back, the Bonnes confront the Flutter with their mothership, but Mega Man overpowers them again and destroys the Gesellschaft.

When Mega Man explores the depths of the Main Gate, he unlocks Sub-Cities across the island. While exploring the three of them, he finds the Bonnes in the Old City and destroys their newest robot, a colossal monster named Bruno. Accepting defeat, the Bonnes leave him, though they plan to steal the treasure of the Main Gate once Mega Man gets it. After using the three keys from the Sub-Cities to access the depths of the Main Gate, Mega Man discovers a stasis chamber for the ancient robot Mega Man Juno, a 3rd class bureaucratic unit from Eden, a space station orbiting above the planet. Mega Man accidentally awakens Juno, who refers to Mega Man as "Mega Man Trigger", and realizes that Mega Man is suffering from memory loss. Juno claims that the island's population needs to be purged so it will be more controllable, and leaves Mega Man in a trap while he engages the program in the deepest depths of the ruin. Mega Man escapes the trap with help from Tron and Teisel and confronts Juno, and despite Juno upgrading to a giant form, Mega Man defeats him. Even with Juno's physical body gone, his last words transfer his backup data into the systems of Eden and confirm the Carbon Purification Process. Data gives new commands to the system, stopping the Purification and deleting Juno's backup data from Eden. Data then reveals to Mega Man that he contains all of his previous memories from when he was Mega Man Trigger. Mega Man had stored his memories into Data as a way to prevent Eden from ever tampering with it. Data promises to restore Mega Man's memory when the time comes. The residents proclaim Mega Man a hero and the Caskett family rides off in the repaired Flutter to continue their journey. Meanwhile, the Bonnes sail on a small boat built by Tron out of the scraps from the other robots, with the colossal refractor from the Main Gate in tow.