During most of the adventure, Luigi and Mario explored Bowser's insides and even helped him secretly because Bowser wanted to stop Fawful too. Fawful took control over his castle and was trying to conquer the kingdom Bowser wanted to. Though Bowser had no idea he had inhaled his sworn enemies, the Mario Bros. helped him in the backstages, with Starlow explaining to him what's going on with his body. She always used her false name Chippy to avoid being recognized while inside Bowser. The Mario Bros. could also use the warp pipes in the Pipe Yard to get out of Bowser's Body and go out on their own missions. Again, Luigi proved to be an invaluable help to Mario, often helping him throughout the adventure. At one point, Luigi even had to rescue Mario from a group of Sockops that had taken him. In order to do that, Luigi made use of a Sockop to traverse a field of thorns.
The unlikely trio eventually engaged the Dark Star in their final battle with the Dark Star itself already having used Bowser's DNA to turn into Dark Bowser. Bowser had to reduce Dark Bowser's HP to 0 so that the Dark Fawful Bug could fully revive him and make him bigger. Bowser then had to punch Dark Bowser's belly to have him spit out the Dark Fawful Bug and return to normal size. After that, Bowser inhaled the Dark Fawful Bug (while Dark Bowser tried to do the same) and (unknowingly) let the Mario Bros. fight it. Once they destroyed the Dark Fawful Bug, Dark Bowser became unstable. Then Bowser charged his punches to deliver the final blows on Dark Bowser until he exploded, freeing the kingdom forever from an age of darkness. The Mario Bros. then met up with a beaten Dark Fawful Bug. They were surprised to see that he survived. However, without a body or the Dark Star to sustain him, he didn't have much time left. With one last psychotic smile, Fawful explodes, hoping to destroy the Marios with it, however it instead released everyone from Bowser's body. Everyone then cheered on Mario and Luigi for saving the kingdom, but the celebration was cut short as Bowser was angry when he saw that Mario and Luigi were in his body, and engages the Marios and Starlow in what was to be another epic battle. As the credits rolled, the battle was shown.