Link is a boisterous boy who actively searches for adventure. To seek those thrills, he joins a pirate ship led by the tomboy captain, Tetra. While at sea, Tetra and her crew come across a dilapidated ship covered in a dark fog. Possibly rumored to be the feared Ghost Ship, Tetra jumps to the mysterious vessel, only to disappear. Link tries to run over to her aid, but he falls into the water and loses consciousness.

Link awakens on the shores of Meruka Island to the cries of a fairy named Ciela, and he is taken to the fairy's grandfather, Oshus. Oshus tells the boy that a sailor named Linebeck might be able to help him find his missing friend. However, when Link and Ciela find Linebeck in the Temple of the Ocean King, they become suspicious of his intentions. Nevertheless, Link will need Linebeck's ship to travel across the seas and gather the Hourglass of Dreams' Sands of Time in order to save Tetra.