The Legend of Zelda: Spirit Tracks is the second Zelda game for the Nintendo DS. The art direction is still cel-shading, but the game have notable changes from Phantom Hourglass with more puzzles and a new mode of transportation by train. You have to draw your route to the next area on the map and then let the train run its course. While the train is moving, caution will be needed to avoid obstacles, animals and enemies on the tracks. In certain dungeons, both Link and Zelda will be playable as they will need to work together to solve puzzles.

Apprentice engineer Link is ready to travel to Hyrule Castle and receive his engineer's license. During the ceremony, Zelda slips Link a note warning him not to trust the Chancellor and to help her reach the Spirit Tower. The land's Spirit Tracks, mystical railway tracks that cover the land, have been disappearing and she suspects that the Chancellor is the cause. While heading to the Tower, the Chancellor intercepts them and proves Zelda's suspicions right: he casts a magic spell on her, splitting her body from her soul. Link and Zelda must work together to return Zelda to normal and save Hyrule once again.