- "Our ship got caught in a storm and sank. When we woke, 'ere we were. Where are we? It all looks so weird."
- — Piratian
The Pirate Ship can be found within the Sea of Storms, trapped by the rough seas and Whirlpools. In a regular game, it can be found in the past, and in a Linked Game, it is found in the present. Once Link obtains the Zora Scale, he is allowed into the Sea, where he can then swim onto the ship.
Inside the ship, Link meets Cap'n, who tells Link of his plight. After Link gives him the Zora Scale, he gives Link the Tokay Eyeball. The Captain informs his crew that they are heading to Holodrum, presumably at which point they become marooned in Samasa Desert.
Once Link travels to Subrosia, he meets Cap'n in the House of Pirates. He informs Link that his ship has been trapped between worlds, the stern of the ship being located just east of the house and the bow protruding from southern Samasa Desert.
After Link obtains the Rusty Bell from the desert and has the Subrosian Smithy polish it, Cap'n and his crew head toward the ship and set sail. They sail out of Samasa Desert into the open ocean, but soon become seasick. They dock just to the west in between a broken bridge at the Western Coast, where it remains for the remainder of the game. This completes the bridge, allowing Link to continue to the west.