While on a walk, Mario discovers a mysterious black sludge M in the Mushroom Kingdom. After being absorbed by it, Mario finds himself in an archipelago of cat-themed islands called Lake Lapcat that have become overrun with black sludge. Upon his arrival, Mario encounters Fury Bowser, a dark version of Bowser that has grown to colossal size. Mario collects a Cat Shine, causing Bowser to retreat. Bowser Jr. appears and pleads for Mario's help to restore his father to normal, and Mario reluctantly agrees.

The two travel across Lake Lapcat in order to obtain Cat Shines, aided by Plessie the aquatic dinosaur. After obtaining a certain number of Cat Shines, Mario gains access to the Giga Bell, a super-powered variation of the Super Bell. The Giga Bell transforms Mario into Giga Cat Mario, a colossal version of his regular cat form, allowing him to battle Fury Bowser.

After using the Giga Bells to fight Fury Bowser several times, Bowser is drained of the sludge which transformed him. Despite this, he remains colossal and out of control, and steals the three Giga Bells. Mario manages to retake the Giga Bells, using all three to turn Plessie into a giant and crush Bowser. Bowser is returned to his normal size, and Bowser Jr. breaks off his alliance with Mario as the two retreat. Mario and the cats of Lake Lapcat celebrate atop the still-giant Plessie. A series of paintings by Bowser Jr. shown during the credits explain that he was responsible for accidentally creating Fury Bowser, having painted his dad's face with his magic paintbrush while he was sleeping as a prank.

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