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The game opens with a disease called "The Blorbs" spreading across the Mushroom Kingdom. Toads that become infected with the disease inflate like a balloon and roll around uncontrollably. A council meeting is immediately called at Princess Peach's Castle to discuss what can be done about the epidemic. Starlow, a representative of the Star Sprites that watch over the Mushroom Kingdom, also attends, as do Mario and Luigi. At the meeting, it is discovered that all those affected had previously eaten a "Blorb Mushroom" given to them by a salesman, who is secretly the mad scientist Fawful. Bowser invades the castle, intending to kidnap Princess Peach, but is defeated by Mario and expelled from the castle, sending him flying outward.

Bowser finds himself in Dimble Wood, where he is tricked by Fawful into eating a "Vacuum Shroom" that gives him the power to inhale things. Immediately after eating it, Bowser begins mindlessly inhaling everything in sight and goes back to the castle, where he inhales Mario, Luigi, Princess Peach, Starlow, and several Toads into his body, the process shrinking all of them to microscopic size. After this, Bowser passes out, and with Peach now gone and the Blorbs incapacitating the majority of the Mushroom Kingdom, Fawful proceeds to take over Peach's castle, while his assistant, the boar-like Midbus, takes over Bowser's castle. Navigating Bowser's body, Mario and Luigi manage to revive him, and he is revealed to have no memory of his mindless rampage; consequently, he does not know that the Mario brothers are inside his body. Bowser only communicates with Starlow, who nicknames herself "Chippy" to conceal her true identity. Bowser begins tracking down Fawful in an attempt to reclaim his castle with the assistance of the Mario brothers and Starlow.

After leading Bowser into a trap, Fawful removes Peach from Bowser's body and kidnaps her, allowing him to take possession of the Dark Star, an evil and powerful entity with a seal that can only be broken by Peach. The Dark Star subsequently creates a barricade preventing anyone from entering Peach's Castle. Mario and Luigi are able to sneak out of Bowser's body together via warp pipe into Toad Town, where physician Dr. Toadley tells them they must gather the three Star Cures in order to create the Miracle Cure, a magical medicinal object that will cure the Blorbs and destroy the barricade. Bowser overhears this and races for the cures himself, only to be trapped in a safe by some of his minions who betrayed him to serve Fawful. Ultimately, the brothers collect all three star cures, and the Miracle Cure destroys the barricade, curing all victims of the Blorbs in the process.