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SpongeBob acquires Mermaid Man's powers when he wears his belt. Unfortunately SpongeBob accidentally puts the Dirty Bubble into a washing machine with the belt, which causes him to split into countless dirty bubbles. SpongeBob has to stop villains such as Manray, The Sinister Slug, The Jumbo Shrimp, Atomic Flounder, and Dirty Bubble, using Mermaid Man's powers to save Bikini Bottom. The story is divided into Acts, each with a different villain trying to wreak havoc on Bikini Bottom: Manray wants to flood Goo Lagoon; Sinister Slug has an evil plan to stop the talent show; Jumbo Shrimp, with the help of Plankton, creates a machine to shrink people; The Atomic Flounder causes chaos in Industrial Park; and The Dirty Bubble returns with the machine the Jumbo Shrimp used in the third act and plans to hit SpongeBob with more Little Dirty Bubbles.
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Critical reception of the DS version was reviewed more positively than this of the PSP, gaining a 7.3 on GameSpot and a 7.7 from IGN, saying that "Developer Tantalus came up with a beautiful 3D engine to make for one of the better-looking games on DS, and publisher THQ put enough love and support into this to make it last long and stand out from the flood of rush-job platformers parents have the choice of this holiday season.".