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In the third installment of the Mario & Luigi series, the Mushroom Kingdom's citizens fall victim to a mysterious disease known as the Blorbs. Upon hearing this news, Peach proceeds to hold a very important meeting in her castle to discuss the matter at hand (along with Starlow, who explains further about the disease itself). Unfortunately, as Peach was proceeding to give said details, Bowser crashes the meeting... twice. He was ejected by Peach (with the help of Starlow) the first time. But Bowser managed to return to the castle the second time, but under the control of Fawful, via eating a Vacuum Shroom. As a result, Bowser inhales everyone at the meeting, including Peach.

Peach is found by Mario and Luigi in the Flab Zone of Bowser's body. Their reunion is cut short, however, when a group of Beta Kretins captures her and takes her deeper into the area. When the brothers catch up and free Peach, the Kretins attack and are subsequently defeated. After the said ordeal was over, Peach begins to inform the two of Fawful's real plot - to take over the Mushroom Kingdom by using an ancient artifact known as the Dark Star, hidden beneath Toad Town. She also informs them that she is the only one who can release the seal on the Dark Star's power. However, while relaying said information to the two about the impending danger, Fawful quickly captures her through the use of an odd invention that enables him to reach into Bowser's body with a hand-shaped beam and then takes her to her own castle (which was also under Fawful's control at the time).

Upon Mario, Luigi, and Bowser finally countering the sources of the "blorbs" threat, along with defeating the Dark Star itself for good, everything in the Mushroom Kingdom returns to normal and Peach is rescued at last. She also manages to regain consciousness as well (Peach was knocked out by the Dark Star's unimaginable power when said threat on the Mushroom Kingdom was undoubtedly imminent). Though Bowser attacked the Mario Bros. and still attempted to kidnap Peach directly after the Dark Star was defeated, Peach still expressed her gratitude toward Bowser for his role in saving the world by sending him a cake.