The map screen also contains Toad Houses where players can visit Toad and receive additional items, and Mystery Boxes where more Star Medals can be earned. Each course contains three hidden Star Medals that are required to unlock certain levels. (The invincibility leaf and the P-wing are only available in regular worlds). The Invincibility Leaf, which appears after the player dies five times in a level, gives Mario invincibility and Tanooki Suit abilities while the P-Wing, which appears after the player dies ten times in a level, sends the player right to the end of the level, near the Goal Pole. Other items include the Boomerang Flower, which allows Mario to throw boomerangs that can collect out-of-reach items and attack enemies the Propeller Box, which allows Mario to reach high places and the rare Prize Box, which gives Mario extra Coins while walking around in it. Super Mario 3D Land utilizes a similar level objective to the aforementioned side-scrolling games, in which the point of each level is to reach and grab the 'Goal Pole' at the end of the level, within the time limit. Mario has also learned two new moves: a barrel roll and a roll jump, the former of which can be used to break blocks in a similar manner to jumping at blocks from below or ground pounding, and the latter allowing Mario to cover much horizontal ground in one jump.

Similar to the older side-scrolling Mario games, the health system revolves around Mario shrinking upon taking damage from enemies or hazards, there is a dedicated 'Dash' button as opposed to using analog input to determine travel speed, and damage as 'Small Mario' results in losing a life. Super Mario 3D Land combines the elements of traditional side-scrolling video game titles, such as linear-based levels, with those of the modern open world titles, such as moving Mario in three dimensions and performing a variety of actions.

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