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Shuffle Mode is a minigame that appears in Yoshi Topsy-Turvy. The objective of this minigame is to play through an endless series of random missions and areas in the game and to get as far through it as possible. There may also be a "Double Mission", where the player must complete two different objectives at once to proceed to the next area. The minigame will end when Yoshi either fails to complete a mission or loses a life. This minigame can be unlocked by completing the main game.
Another more difficult version of Shuffle Mode called Shuffle Mode EX also appears in the game.