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All controls use the stylus, and one uses the microphone.
- Slide Stylus: Creates clouds for Baby Mario/Yoshi to move on.
- Draw Circle: Creates bubble. If an enemy is caught within the bubble it will turn to coins.
- Blow into Microphone: Blows away all clouds created with the stylus.
- Tap Screen: Shoots egg in direction of cross hairs
- Tap Yoshi: Makes Yoshi jump. If already in the air, causes him to flutter kick, sending him higher.
- You cannot trap certain enemies, especially ones with spikes, in a bubble.
- A deformed or very big circle will not result in a bubble.
- Each game type has the same controls, just different goals
- During the sky sections of the game, you direct Baby Mario's movement by drawing clouds on the bottom screen.
- Circling enemies will turn them into coins inside bubbles, which can then be thrown to Baby Mario to be collected.
- You can also circle coins themselves, and do the same thing with them.
- Once you reach the end of the sky section, Yoshi takes over moving Mario during the ground section.
- Everything possible in the sky is possible on the ground.
- There are a few controls only possible while on the ground.
- Different color Yoshis have varying speeds, and starting amount of eggs once the ground is reached.
- Yoshi's color depends on amount of points collected in the sky section
- You throw eggs to collect coins and defeat enemies.
There are four different gameplay types to choose from. Each one has its own unique goal, but all the controls remain the same, and each mode has you go through the sky section in the game.
- Sky Section: Guide Baby Mario safely to the ground
- Score Attack Mode: Make it to the stork at the end of the level while earning as many points as possible.
- Marathon Mode: Carry Baby Mario as far as possible, switching off Yoshis at every 1000 distance mark.
- Time Attack Mode: Save Baby Luigi as fast as possible by hitting the Toadies twice each.
- Challenge Mode: Race against the timer to get as far as possible. Every enemy killed will add more time to the timer.