Bowser has released his new space castle, and now Mario, Luigi, and Yoshi must stop him. However, this special airship, the Lunar Mushroom only supports one passenger and to defeat Bowser, they need eight of the Special Orbs. The eight wielders of the Special Orbs, including Mario, Luigi, and Yoshi themselves, then must take part in a hand-to-hand fighting tournament, with the winner taking all the Special Orbs. The participants, in order of combat, are:
- Princess Peach
- Captain Waddlesword
- Donkey Kong
- Sky the Yoshi
Whichever character the player is controlling is cloned by Kamek during their battle (presumably by copying their DNA), so that the player fights all eight of them. For instance, if the player controls Mario, then in the eighth battle, Kamek will create a differently-colored clone of Mario.
After arriving at Bowser's space castle, Kamek challenges the heroes to battle him at the Castle Rooftop. After defeating him, Bowser's space castle begins to fall apart as Bowser challenges the victor (the round must be finished to complete the story). Unlike other battles in the game, the player only gets one shot to take down Bowser and also has fifteen seconds to defeat him.
The victor escapes Bowser's space castle before it explodes, however, the post credits scene shows Bowser and Kamek also escaped the explosion and head back to Earth.
- Mario (can transform into Powerful Mario during the final matches) Stage: Pipe Junction
- Luigi Stage: Lost Forest
- Princess Peach Stage: Mushroom Kingdom
- Yoshi Stage: Donut Plains
- Donkey Kong Stage: Jungle Japes
- Wario Stage: Pokey Desert
- Sky the Yoshi Stage: Sky World
- Captain Waddlesword Stage: Sherbet Land
Added in the GameCube version
- Princess Daisy-Press Start on Princess Peach
- Bowser-Press Start on Sky the Yoshi
- Kamek-Press Start on Mario
Lakitu appears in this game as an announcer.