Mario and Peach's vacation to the tropical Isle Delfino is rudely interrupted by a shadowy doppelganger, who attempts to frame Mario by polluting the island and stealing the Shine Sprites, also kidnapping the princess in the process.

After being found guilty by the island natives, Mario is tasked with cleaning up the island and retrieving the stolen Shine Sprites. Together with his new water-pump ally FLUDD, Mario must restore the island, uncover the truth behind this "Shadow Mario," and save Princess Peach.

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