The game follows the adventures of Link and Tetra, the leader of a band of pirates, as they discover a ghost ship in dense fog. Link falls into the ocean when Tetra gets into trouble, and he wakes up alone on the shore of a mysterious island. Throughout the game, Link collects sand for his Phantom Hourglass, which allows him to explore deeper and deeper into a time-limited dungeon in his quest to find Tetra.

In both style and characters, The Legend of Zelda: Phantom Hourglass echoes the smash-hit The Legend of Zelda: The Wind Waker for Nintendo GameCube. But the inviting, easy-to-understand story and ease of control will attract casual and younger players who might be new to Zelda games. The game features a two-player battle mode that can be activated via the game's Wi-Fi connection, as well as the ability to play the entire game with only the Nintendo DS touch screen.