The game's story follows that of The Wind Waker, focusing on series protagonist Link's journey to save his friend Tetra from the story's antagonist, Bellum, with the help of Captain Linebeck and his ship, the S.S. Linebeck.
Spillets historie følger af The Wind Waker, der fokuserer på Links rejse for at redde sin ven Tetra fra historiens antagonist, Bellum, med hjælp fra kaptajn Linebeck og hans skib, S.S. Linebeck.