When boys of Outset Island come of age they are customarily dressed in green, like the Hero of Time. The elders hope to instill the courage of the Hero of Time in the children. It is Link's birthday as The Wind Waker opens, and he receives the familiar green clothes and cap. Aryll's present to Link is permission to use her telescope, and as he looks through it, he spots a large bird, carrying a girl to a nearby forest. After retrieving a sword, Link sets out to investigate. Link rescues the girl, only to have Aryll kidnapped by the bird as it returns.
The girl rescued in the forest is Tetra, captain of a pirate ship. At Link's request, they sail to the Forsaken Fortress, where a mysterious figure is holding Aryll and several other girls. Following an unsuccessful raid, Link is captured by the Helmaroc King and hurled into the ocean. A talking boat called the King of Red Lions rescues Link and tells him that the master of the Forsaken Fortress is Ganon, the evil of legend. After purchasing a sail, Link travels to Dragon Roost Island at the King of Red Lions' suggestion.
Once at the island, the King of Red Lions instructs Link to locate Dragon Roost Island, home of a dragon named Valoo and the Rito tribe, a bird-like race, and ask them for a jewel called Din's Pearl. Link receives the Wind Waker, a baton able to control the wind, from his boat and sets out towards the dwelling of the Rito tribe. Link learns that Prince Komali has Din's Pearl, but is unwilling to relinquish it. Prince Komali is of the age when members of the Rito tribe traditionally climb to the top of Dragon Roost Island to get a scale from Valoo, which allows a Rito to grow wings. However, Valoo has grown violent and unpredictable and Prince Komali is fearful to attempt the journey. He agrees to give Link the pearl if Link can calm Valoo. With the help of Rito tribe member Medli, Link makes his way to Valoo and defeats Gohma, the monster that had been upsetting the dragon. Afterwards, Link receives Din's Pearl from Prince Komali, who is finally ready to ascend the mountain and gain his wings.
The King of Red Lions has Link sail south to the Forest Haven to ask the Deku Tree for Farore's Pearl. Inside the haven, Link saves the Deku Tree from a group of ChuChus and is introduced to the Koroks, spirits of the forest. Aware that Ganondorf has returned, the Deku Tree agrees to give Link the pearl after the annual ceremony to replenish the forests. Linder, one of the Koroks, enters and informs the Deku Tree that fellow Korok Makar has fallen into the Forbidden Woods. The Deku Tree, believing that Link's appearance is not a coincidence, asks Link to help. Link rescues Makar from a large plant monster named Kalle Demos and returns to the Forest Haven. The ceremony is completed and Link receives Farore's Pearl.
Link then travels to Greatfish Island seeking Jabun, a great water spirit, but finds that the island has been demolished by Ganondorf. After a trip to Windfall Island to obtain bombs, Link returns to Outset Island and blows open the entrance to a cave in which Jabun is hiding. During a conversation between Jabun and the King of Red Lions, Jabun gives Link Nayru's Pearl.
Link takes the three pearls to the three Triangle Islands, inserting one into a statue on each island. An image of the Triforce appears and the Tower of the Gods rises from the sea in the center of the islands. Link enters the tower, where he battles Gohdan to prove his worth. After defeating Gohdan, a ring of light appears on the surface of the water below. Link sails into the ring of light and is taken beneath the waters to Hyrule Castle, which is overrun with enemies and frozen in time. Link descends a hidden staircase, where he finds the Master Sword, the evil-repelling blade that the Hero of Time used to seal Ganondorf. By removing the sword, Link awakens the castle and all enemies inside. He destroys the enemies and returns to the surface.
Restoring the Master Sword
With the Master Sword in hand, Link returns to the Forsaken Fortress and joins Tetra and the pirates. He frees the captives and kills the Helmaroc King in a dramatic rooftop battle, but is easily defeated by Ganondorf. Ganondorf tells Link that taking the Master Sword has fully lifted the seal, unbinding his full power; furthermore, the Master Sword has lost its power to repel evil. Ganondorf raises his sword to kill Link, but Tetra intervenes. Ganondorf grabs Tetra, and is about to snap her neck when the Triforce of Power responds and he notices that Tetra is wearing a piece of the Triforce of Wisdom as a necklace. As he calls her Princess Zelda, Quill and the now-winged Prince Komali fly in and take Link and Tetra away. Valoo swoops into view, breathing fire and sending Ganondorf's room up in flames.
Link and Tetra sail back to the castle at the bottom of the sea and descend the staircase, where they meet King Daphnes Nohansen Hyrule, the king of Hyrule and the voice of the King of Red Lions. He tells Link and Tetra that the prayers of the people in the legend were answered — the gods sealed Ganondorf and all of Hyrule with him by flooding the kingdom with a torrential rainstorm, ordering those chosen to take refuge on the mountaintops. The King takes out a piece of the Triforce of Wisdom, which completes the piece in Tetra's necklace, causing her to transform into the more traditional appearance of Princess Zelda.
At Dragon Roost Island, Link plays the Earth God's Lyric to Medli, which awakens the knowledge that she is the sage of Earth, able to help restore the power of the Master Sword. Link and Medli battle through the Earth Temple and defeat a massive Poe named Jalhalla. Medli begins to pray, restoring some power to Link's sword. Link leaves Medli to continue praying and sails to the Forest Haven. He finds Makar and plays the Wind God's Aria, giving Makar the realization that he is the Sage of Wind. They travel to the Wind Temple and defeat the sandworm Molgera. Makar prays and restores the Master Sword's full power.
Link then goes on a variety of quests to find and decode eight nautical charts that mark the locations of the pieces of the Triforce of Courage. Link raises the pieces from the sea and restores the Triforce of Courage, which then dwells inside Link, marking him as the Hero of Winds.
Confrontation with Ganondorf
With the restored Master Sword and the Triforce of Courage, Link returns once more to Hyrule Castle, where Zelda disappears before him. Link breaks through the barrier beyond Hyrule Castle and enters Ganon's Tower, where he reaches Zelda and fights large puppets created by Ganondorf. When these are defeated, Ganondorf reveals himself to Link, claiming that Link is the reborn Hero of Time. Link follows Ganondorf to the roof of the tower, where Ganondorf tells Link why he wanted to rule Hyrule. He says that his country lay within a desert, where the searing winds of the day and the frigid gale of the night always brought death with them, whereas the cool breeze of Hyrule brought life to its people. He coveted those winds, wishing to rule a land that wasn't destroyed by them. Ganondorf remarks that it must be fate that has allowed him to bring all of the pieces of the Triforce together again, just as he had with the Hero of Time. The three Triforce pieces are extracted from Ganondorf, Link, and Zelda and combine to form the complete Triforce. Ganondorf demands that the gods to expose Hyrule to the sun once more, under his control. Before he can reach the Triforce, however, King Daphnes suddenly appears, touching the Triforce. He asks the gods of the Triforce to give Link and Zelda a future and to wash away Hyrule. Finally, he asks for everyone's fates to be fulfilled, and that Ganondorf may drown along with Hyrule. The Triforce then splits apart and disappears as water from the ocean above begins to pour down all around the tower.
Knowing he had just heard his own death sentence ushered through the power of the gods, Ganondorf laughs maniacally, calling the idea of hope for the children "foolishness." He then draws his swords, wishing to deny King Hyrule's wish and prove the power of the Triforce wrong, and begins battling Link (this can be interpreted as a signal that Ganondorf's sanity is fading). Zelda assists by using Link's bow and shooting Ganondorf with Light Arrows. After Ganondorf knocks out Zelda, Link has to fight him alone without the help of the light arrows. Eventually Princess Zelda regains consciousness and Link has to reflect the light arrows with his shield in order to hit Ganondorf. Once Ganondorf is stunned, Link launches his final attack by rolling around Ganondorf, jumping in the air holding the Master Sword downward, then stabbing him in the forehead, turning him to stone. After a conversation with the King of Hyrule, Link and Zelda float to the surface in a bubble, leaving Ganondorf and the king to be buried underwater with Hyrule. Link and Zelda sail away in search of a new land — with the wind as their guide. This scene marks the beginning of the DS Zelda game, Phantom Hourglass.