As the rest of the adventure slides, Mario and Luigi travel until they find Bowser knocked out in a island of trash. After fighting Junker, they go back into Bowser and wake him up from his back pain. After going through the castle all to finding the Dark Star awakening and Fawful becoming Dark Fawful, who is sent flying by Bowser. enters Bowser, who copies his DNA, but is incomplete thanks to the Mario Bros. and combines with to create .
While Bowser is fat, Mario and Luigi find Peach in the , who is attacked and kidnapped in front of them by . After a long chase, Mario and Luigi trap and defeat Alpha and Beta Kretin, freeing the Princess. Peach, after the boss battle, tells them that Fawful probably wants the Dark Star, so he can control the Mushroom Kingdom. She also explains that Peach herself is necessary for this process. As they get to the end of the Flab Zone, Peach is taken out of Bowser's Body by Fawful and is once again kidnapped. Meanwhile, Midbus gives Bowser a treadmill to lose his extra pounds on.
|Trip||Enemy Effect||This effect makes either Mario or Luigi trip over, stopping them from avoiding a single attack. There is a rare chance that when it is their turn, they will not get up and attack.|
|Dizzy||This effect causes Dizziness to Mario, Luigi or enemy. They will not be able to attack or dodge for a turn.|
|Burn/Char||This effect is similar to the Dizzy effect, but actually hurts Mario, Luigi or an Enemy. The effect ends after being hit either once or twice.|
|Mini||This effect makes either Mario and Luigi very small. It makes them inflict less damage. When in the dream world, using the jump or hammer attack when mini still causes the Luiginoids to be normal size.|
|Pow Up||Increase Effect||This effect increases the Power of Mario or Luigi. It can combined with the other increasing effects.|
|Def Up||This effect increases the Defense of Mario or Luigi.|
|Speed Up||This effect increases the Speed of Mario or Luigi, allowing them to attack more regularly because they are faster than the enemies.|
|Pow Down||Decrease Effect||This effect decreases the Power of Mario or Luigi. It can combined with the other decreasing effects.|
|Def Down||This effect decreases the Defense of Mario or Luigi.|
|Speed Down||This effect decreases the Speed of Mario or Luigi, making the enemies attack before Mario and Luigi.|
Mario and Luigi are found inside Bowser, who is knocked out in . The Bros. and Starlow help Bowser get his castle back from Fawful. Along the way, Bowser meets and and gets the ability of the Vacuum block. Mario, Luigi and Starlow aids Bowser in his trips, while they travel to various parts of his body. When Bowser finally reaches his castle and reclaims it, Bowser is grown fat from eating high-calorie foods from the after winning the fight against , a giant pig armadillo hybrid.
Mario and Luigi appear again in . A new disease, the , which make Toads grow to a giant size, has affected the Mushroom Kindgom citizens from , who is selling Blorb Mushrooms. Mario and Luigi attend a meeting that is disrupted when Bowser barges in. Bowser then fights Mario. After defeated, Bowser receives a from . The mushroom makes Bowser inhale everything, including Mario, Luigi, Starlow and the Princess.