Whilst exploring the Mushroom Kingdom, Mario, Luigi, Princess Peach, and Toad come across a strange clear pipe, which a curious green fairy-like creature, called a Sprixie, pops out of. Suddenly, Bowser appears and captures the fairy before escaping through the pipe. Thus, Mario and friends enter the pipe to pursue Bowser, and find themselves in the strange new Sprixie Kingdom as they search for the Sprixie, along with some of her other companions.

After rescuing the final Sprixie, Mario and co. get ambushed by a supposedly defeated Bowser, who re-captures all seven Sprixies again, and retreats to his final castle. After powering up with the game’s two new power-ups, Bowser engages the heroes in a final battle, but is defeated. All dressed in their Cat Suits, the four heroes leave the Sprixie Kingdom as the citizens wave goodbye. Bowser meanwhile, is now trapped in a bottle as punishment.