Phantom Hourglass is an action-adventure game, and its gameplay is structured similar to other games in the The Legend of Zelda series. The player controls the protagonist, named Link, as he explores the world to find new items, information, and allies to free Tetra and defeat the evil of Bellum within the game. As the game follows chronologically after The Wind Waker, the game is primarily divided into two major game play sections: sailing between islands, and exploring the islands and their dungeons on foot.
When on land, the game shows a map of the area on the top screen, and a 3D top-down view of Link and his nearby surroundings on the lower screen. At some points during the game, usually during boss battles, a 3D view is shown on both screens, allowing the player to have a wider view of their surroundings, or show an enemy from a different angle. At nearly any time, the player can bring down the map to the lower screen and draw on it, typically to make notes but also to identify locations of objects for later reference or to control certain aspects of the world. The player controls Link through the stylus, moving him around by pointing to the sides of the screens, and interacting with objects and people, or attacking foes by pointing at them; other motions with the stylus can be used for additional moves and attacks. Tools common to the Zelda series such as the boomerang, grappling hook, and shovel are acquired through the game, and are used to open new passages to acquire additional treasures, all used by either pointing or drawing with the stylus. The game also uses the microphone for some events, including blowing out fires and defeating certain types of monsters, and other aspects of the Nintendo DS system, such as closing the unit to create an imprint on a map.
To travel between islands on the Great Sea, the player is given control of a paddle steamer called the S.S. Linebeck. The player can plot a course by drawing on a sea chart, redrawing the course to make alterations if needed, and then while in voyage, can shoot at enemies attacking the ship using the cannon (once obtained) and jump to avoid obstacles that may appear. Throughout the game treasure maps can be found, this creates a red X on the sea chart, plotting where the treasure lies. The player can then salvage these treasures from the ocean floor using the Salvage Arm (once obtained). When salvaging for treasure, a view of the undersea environment is shown on the bottom screen, and the player can control the speed and movement of the arm with the stylus. By dodging the mines scattered under the sea, the treasure can be brought back up to the ship. Once the player receives the Cyclone Slate from the chief frog, they are able to travel to other places in the ocean via cyclones by simply drawing the appropriate symbols on the Slate. These symbols can be obtained by hitting smaller golden frogs in the sea with cannonballs.
Over the course of the game, the player can obtain ship parts through treasure chests, salvaging from the bottom of the ocean, prizes, and mail. These ship parts can be used to customize the S.S. Linebeck. By collecting ship parts from the same set, the player can increase the stamina of the ship, giving it extra health. The ship’s health can be expanded to a maximum of eight hearts, but this can only be obtained by collecting the rare “Golden Ship” parts.
The majority of Zelda games preceding Phantom Hourglass have had the player collect Pieces of Heart to increase Link’s health. In Phantom Hourglass, Pieces of Heart are not scattered throughout the land as in previous games, but full Heart Containers are rewarded after defeating bosses, and some also for mini games, similar to the original game, The Legend of Zelda.
The game possesses a number of stealth elements. In certain dungeons near-invincible sentries known as Phantoms, who can send Link back to the beginning of the room if their swords make contact with him, may roam the floor, with their location and direction visible to the player on the map, and will chase Link down if he is spotted or makes a loud noise. However, special areas on these floors allow a safe haven for Link to stay undetected in, even if he was detected just moments before. These special areas are called “safe zones” and play a crucial role in the main dungeon, the Temple of the Ocean King. This temple is filled with a miasma that will sap Link’s life unless Link stays in these special areas or time remains in the Phantom Hourglass.
The Phantom Hourglass is crucial for survival in the Temple of the Ocean King. It contains sand called the “Sand of Hours” and is able to protect Link from the temple’s curse as long as there is time remaining in the Hourglass. If Link is defeated by a Phantom, some sand in the Hourglass is lost and Link must restart at the beginning of the floor. Additional Sand of Hours can be obtained by defeating bosses and salvaging it from the bottom of the ocean. The Phantom Hourglass’ Sand of Hours can be expanded to 25 minutes.
A multiplayer battle mode is also included in Phantom Hourglass. This battle mode is a one-on-one multiplayer game dubbed “Hide-and-Go-Seek” by Eiji Aonuma. In an arena, one player takes on the role of Link, while the other player, on defense, controls three Phantom Guardians. Players of both sides are aided by power-up items that shortly appear on the playing field, such as the Pegasus Shoes, power gloves, a Decoy, a Time Increase and turning on Wind Walls.
Link’s goal is to grab a Force Gem from one of the many zones and carry it to his own base at one side of the arena. The other player, controlling the three Phantom Guardians, must try to find and catch Link before he scores any points. When Link is caught, or if the turn-time has passed, players switch sides. A game consists of three rounds, and in each round, each player takes a turn at both sides. The maximum length of one whole multiplayer game is twelve minutes, assuming Link does not get caught and no time bonuses are acquired.
In addition to playing to win, players can earn Big Plays by doing certain things in the battle mode. For every four Big Plays a player unlocks, they earn a gift in the story mode. They must receive a letter, then pick up the gift on Cannon Island.
Set some period after The Wind Waker, Phantom Hourglass opens with Tetra and her pirate crew along with Link encountering a Ghost Ship claimed to have taken sailors and residents of the local islands in an area of the Great Sea. The crew discovers the ship, but when Tetra goes aboard to explore, she disappears; Link attempts to follow her but ends up adrift in the ocean.
Link later wakes up on a strange island through the help of the fairy Ciela (who has some amnesia about her past) and an old man named Oshus, who help Link on his quest to find the Ghost Ship and reunite with Tetra. To that end, they enlist the help of the reluctant Captain Linebeck and his ship after saving him from the Temple of the Ocean King; Linebeck only offers to help with the expectation of finding treasure along the way. [not in citation given] Link discovers that to learn of the Ghost Ship’s position, they must find the Spirits of Courage, Wisdom, and Power, using maps and clues hidden in the Temple of the Ocean King. However, to overcome the evil forces in the Temple, Link must make use of the Sands of Hours within the Phantom Hourglass and possessed by other creatures around the islands to prevent his life force from being drained. With the aid of the Hourglass, Link is able to locate and ally with the Spirits of Wisdom and Power easily, but the Spirit of Courage he finds looks exactly like Ciela. Oshus explains that Ciela is actually the Spirit of Courage. Ciela is then reunited with the rest of her self, and awakens as the Spirit of Courage. With Link, they proceed to the Ghost Ship. He succeeds in his attempt to rescue Tetra with the help of the three Spirits, but finds that Tetra has been turned to stone. Link wants to find a way to save Tetra, but Linebeck refuses to help further, as there was no treasure. Oshus then reveals that he is the Ocean King, and that he and Ciela had to take their present forms to hide from the life-eating monster Bellum, who is the cause of the Ghost Ship, Tetra’s statue form and other evil in the local area, and has taken residence at the very depths of the Temple. Linebeck quickly changes his mind as soon as Ciela and Oshus promise to grant him one wish if he helps Link complete his quest to defeat Bellum and save Tetra.
Link learns that the only way to defeat Bellum is to forge the Phantom Sword from three unique, “pure” metals around the local islands called Crimsonine, Aquanine, and Azurine. After collecting the materials and forging the Phantom Sword, Link descends to the bottom level of the Temple, and initially appears to defeat Bellum. Tetra is freed from her statue form and revived, but before the group can celebrate, Bellum reemerges from the ocean depths and takes Tetra again. In the ensuing battle between the S.S. Linebeck and the Ghost Ship, Linebeck’s ship is sunk with Oshus still on board, and Link and Tetra are captured. Linebeck reluctantly picks up the Phantom Sword and is able to free Link and Tetra at the cost of his own freedom, but is able to give Link back the Phantom Sword before becoming possessed by Bellum, turning him into a huge Phantom. Link is ultimately able to fully defeat Bellum without harming Linebeck.
As the adventure closes, the sand from the Phantom Hourglass is released into the sea. Oshus, now in his true form of a white blue whale, readies to depart with the Spirits, while Linebeck, surprising everyone, wishes not for treasure but for his ship back. After everyone says their goodbyes, Link and Tetra find themselves back on the pirate ship, where it seems only ten minutes have passed for the rest of the crew and they insist that the events were all just a dream. However, Link still possesses the now-empty Phantom Hourglass, and spies Linebeck’s ship on the horizon, knowing full well that his adventure was real.