Based on the game for the Nintendo Wii U, the Nintendo 3DS version of Captain Toad: Treasure Tracker contains all the content from the original game in addition to some new levels from the Nintendo Switch game Super Mario Odyssey.

The goal of Treasure Tracker is to navigate Captain Toad (who was introduced in Super Mario 3D World for the Nintendo Wii U) to the treasure in each level whilst avoiding enemies and collecting green starts, of which there are three in each stage. Stages are deliberately small and it is often up to the player to move parts of the stage using the touchscreen and sometimes blowing into the 3DS's microphone to guide Captain Toad to the treasure. Captain Toad also cannot jump, as is the norm in previous Mario titles, is slow to walk/run and has no way to defend himself from enemies without the aid of a pick axe power up which will run out in a limited time upon collection. 

Toadette is also an unlockable character as a reward for the player's progression through the game, although this is only a cosmetic change, as she has the same abilities and limitations as Captain Toad. 

The game also has some Amiibo functionality, if a Nintendo Amiibo is scanned of Toad, a new Hide-and-Seek mode is unlocked, in which the player must seek out a small pixelated Toad which is hidden in every level, but will only become available after the player has beaten the original level first. If any Nintendo Amiibo is scanned other than Toad, it will grant the player an extra life. 

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