- "One ill-fated day, misfortune befell me and my boat was destroyed. Clinging to the wreckage, I drifted at the whims of the waves... That's when I saw this monstrosity. This foul ship, veiled in mist and fading in and out of sight like something of another world... Yes, my young sir... 'Tis none other than the Ghost Ship!"
- — Lenzo
This strange, paranormal ship sails under the night sky in a different sector of the Great Sea each night according the lunar cycle until it is freed from its curse. The only one able to board the ship and lift the curse is the one who obtains the Ghost Ship Chart, which is hidden in a secret maze in Diamond Steppe Island. Otherwise, the ship fades away before anyone can get close enough to enter it.
The appearance of the ship is similar to Tetra's ship, except that is smaller and transparent, with a tattered sail and flag. On it's bow is a carving of what appears to be a person praying, and surrounding it are balls of blue flame. Whenever Link is in the same region as the Ghost Ship, the sky fills with dark clouds but no rain. When the Ghost Ship draws near, a haunting melody plays.
The interior of the ship is similar to that of a submarine's, except the wooden beams around are broken up, a blue mist covers the floor, and on both sides of the floor are four skulls lined in a row. Also, if Link looks up, he notices that the cracked part on the ceiling (the left side) is completely covered in objects that look like ghosts moving over the ceiling. There is also a small beam of light on the far right side of the ship, containing a lone flower. Interestingly, a painting of a man can be found in the room containing the treasure. When seen from afar, the painting depicts a face with a demonic smile. As Link approaches it, however, the face's smile in the painting diminishes, and when Link is as close as can be, the face is expressionless.
The Ghost Ship can be found in different places depending on which phase the moon is in. The lunar phases are depicted in the Ghost Ship Chart. The ship appears near the Five-Star Isles (Waxing Crescent), the Star Belt Archipelago (First Quarter), Greatfish Isle (Waxing Gibbous), Crescent Moon Island (Full Moon), Diamond Steppe Island (Waning Gibbous), Bomb Island (Last Quarter) and Spectacle Island (Waning Crescent). At some of these islands, if Link spreads All-Purpose Bait near a Fishman, the fish will warn him not to come when the moon is in the island's respective phase. Lenzo took a pictograph of the Ghost Ship during his adventures across the Great Sea and displays it with the rest of his pictograph collection on the second floor of his shop on Windfall Island.
Link eventually uncovers the chart and enters the Ghost Ship by sailing right into it. Inside, two Poes and a Wizzrobe, which can summon Stalfos and ReDeads, attack him as soon as he enters the central room. Once he eliminates all the enemies aboard the ship, a Treasure Chest containing a Triforce Chart (Shard in the HD version) appears. Once Link claims the treasure, a demonic screaming/laughing voice sounds throughout the ship. The screen fades and Link awakens aboard the King of Red Lions, suggesting that the experience may have been a hallucination.
After the curse is broken, the ship permanently disappears from the seas, never to reappear again.