Ghost Ship (Dungeon)

The Ghost Ship has appeared on two different occasions. It is found in The Wind Waker and in Phantom Hourglass. It should be noted that these two incarnations are unrelated to each other. Paragraph by Link 997
 * A way you can tell that they are different is the shape and features. Phantom Hourglass Ghost Ship has a skull on the front of the ship and has no spirits floating arouund. Also, the ghost ship is visible in day, opposite to The Wind Waker. The other ghost ship has more of a gloomy appearance looking more like a real pirate ship with blue spirits haunting the decks.

The Wind Waker
In The Wind Waker, the Ghost Ship haunts several islands of the Great Sea during the night. It will appear at several different locations depending on the current state of the moon. The ship is doomed to sail the Great Sea until freed from its curse, and only the one holding the Ghost Ship Chart, hidden on Diamond Steppe Island, can enter the ship and free it from its curse. However, the souls of those who are still trapped on the ship will try to stop anyone who boards it.

According to Lenzo, the sailor who made the Ghost Ship Chart was following the frightening vessel across all of its destinations, drawing a map of its movements. When the map was done, he suddenly died. Interestingly, Link does not die if he continuously visits the Ghost Ship. In fact, there is actually nothing about the ship that can damage Link, except the enemies within; even so, for some reason, the fishmen warn him steer clear of the ghostly vessel. The Ghost Ship appears at the following islands in this order: Crescent Moon Island, Diamond Steppe Island, Bomb Island, Spectacle Isle, Five-Star Isles, Star Belt Archipelago and Greatfish Isle. Because of this, there's no night during which the ship does not appear in the Great Sea. The battle on the Ghost Ship always starts against a Wizzrobe and two Poes, however the Wizzrobe is able to summon more enemies into the battle; namely ones that are undead, such as ReDeads and Stalfos.

After defeating all the enemies within the ship, Link will be able to climb up a ladder to get to a chest which will contain a Triforce Chart. In this small room there is an engraved face on the wall that seems to have a wide, eerie smile from afar. However when Link approaches it the face quickly changes to that of an expressionless, normal face. Also notably, the camera zooms in closer to Link once he is closest to the face, seemingly and suspiciously to give the player a better view of the face to show the contrast.

After Link collects the Triforce Chart hidden within, the Ghost Ship will stop roaming the seas and disappear entirely.

Phantom Hourglass
The Ghost Ship is a plot device, dungeon, and boss battlefield in Phantom Hourglass. At the beginning of the game, it appears within a ghostly fog. Tetra boards it and shrieks once she is out of sight of the others, prompting Link to follow her in an attempt to rescue her. However, he instead falls into the ocean and is taken to the World of the Ocean King. He then searches for a ship captain who will give him a ship to use to chase the Ghost Ship. As a result, he comes across Linebeck, who agrees to help him find the ship with the ulterior motive of finding the riches inside.

After Link has received a bomb cannon for his boat, the Ghost Ship will soon reappear. Link attempts to follow it, but soon becomes lost in the fog. After traveling to Molida Island to find the path he must take, he is able to get away from it, although the fog does not dissipate until Link rescues Tetra from the ship.

After Link has obtained Leaf, the Spirit of Power, Neri, the Spirit of Wisdom, and has caused Ciela, the Spirit of Courage, to regain her memory, he once more sails into the fog. This time, he locates and boards the Ghost Ship, which is filled with Skulltulas, Reaplings, and other undead enemies. Once inside, he must reunite the four Cubus Sisters, who reveal themselves to demons. They then challenge Link to a game of Dead Man's Volley, after which Link is given the Ghost Key to open the door leading to Tetra's whereabouts.

When Tetra is rescued, Oshus reveals himself to be the Ocean King, and explains that the Ghost Ship is actually a way for Bellum to get victims. He spread rumors of a great treasure within the ship to lure people there.

After Bellum is defeated within the Temple of the Ocean King, he takes Tetra again and takes control of the Ghost Ship. Here, Link sails alongside it, launching bombs at Bellum's eyes. Eventually, it sinks, and the final boss battle takes place on its remains. After the game's credits, Link and Tetra awaken on the mysteriously repaired Ghost Ship. They go back onto their own ship, and the Ghost Ship soon disappears without a trace.

Trivia

 * Although not referring to it by name, the Shadow Temple in Ocarina of Time houses an uninhabited ship in the last floor; said to carry its passengers to "the other world", it begins to travel across what seems to be an extremely murky river (except it has no liquid whatsoever) as soon as Link plays Zelda's Lullaby after boarding it. This could possibly mean to the underworld.
 * In The Wind Waker, the only enemies Link seems to encounter aboard the Ghost Ship are undead types, save for Wizzrobes. This is most likely because it is, in fact, a ghost ship and can only house the undead. Wizzrobes are inside probably due to their use of magic.
 * The Ghost Ship has a background theme in The Wind Waker; however, it can't be heard during the Pause Screens (nor when Link approaches too much to it and makes it disappear).
 * Looking through the missing part of the Ghost Ship's roof in The Wind Waker, Link can see a pattern of ghosts floating around. A very similar background pattern is found in Super Mario Galaxy's Ghostly Galaxy.
 * In The Wind Waker, the Ghost Ship and Tetra's Ship have identical models.
 * In the Ghost Ship in Phantom Hourglass on floor B2 in the southwest corner, after the spikes have retracted, the spikes can be seen under the floor; it is possible that this was overlooked by the developers.