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- Lift Wii Remote up - jump
- A - Punch, Interact with things
- Shake Wii Remote - Spin
- B - Switch characters
- 1 - Use power-up abillity
- 2 - See menu
- Nunchuk joypad - Move
- Z - Crouch
- C - Adjust camera angle.
Mario, Luigi and Peach are enjoying a picnic in the garden of Peach's Castle, where a large blue portal sucks them into nowhere. They wake up to find themselves in the Mushroom Kingdom in the future. Then, a gold Toad takes them to the castle, where the Mushroom Kingdom is ruled by The Master. They meet him and when they are trying to figure out what happened, a dark figure attacks Peach. Peach survives, and remains in the castle. Mario and Luigi leave and try to find where the dark figure came from, when a hut appears out of nowhere. They go inside and meet an elderly Toad. They tell him what happened and he says that the only thing strong enough to defeat it would be the Rainbow Spheres, which have been scattered around the different 'islands'. So Mario and Luigi go on a quest to get them and save the Mushroom Kingdom.
- Mario - Default character.
- Luigi - Used only sometimes, or after beating the game. Is faster and jumps higher, but is harder to control.
- Peach - Used sometimes, or after beating the game. Floats down after jumping and hits with a parasol.
While going through the islands, Mario finds special power-ups. The power-ups are found in an island that is like the power-up. They are a special sphere.
- Mole Mario - Can dig into the ground and into lower earthy tunnels.
- Cloud Mario - Moves like Boo Mario. Can rain on things to put out fires.
- Monkey Mario - Can climb vines and attack with his tail.
- Dry Mario - Is immune to most attacks, and can separate into bones.
- Electric Mario - Can shoot electricity and is invincible to physical attacks.
The islands are set out like in Super Mario 64. Mario uses a teleporter to get to all the islands. Key cards, that let Mario access other islands, are collected after defeating a main boss.
- Mushroom Kingdom - This is the first place visited. The Master's castle and Toad's Tent are here.
- Base Island - A small Island. This is the first Island with enemies.
- Earth Isle - Introduction of Mole Mario
- Toy Island - a bright Island with bouncy enemies.
- Sky Isle - Introduction of Cloud Mario
- Isle of Music - A strange Island with large musical instruments.
- Jungle Island - Introduction of Monkey Mario
- Yoshi's Island - An island where Yoshis live.
- Isle of the Sandlands - A desert Island
- Dry Isle - Introduction of Dry Bones Mario
- Splash Island - Set in breathable water.
- Electric Isle - Introduction of Electric Mario
- The Hideaway - The island where the final boss is set.