Set 100 years after the events of Ocarina of Time, The Wind Waker places the hero Link in a sea scattered with several islands, which necessitates frequent sailing and naval combat. Link lives with his grandmother and younger sister Aryll on Outset Island, one of the few inhabited islands of the Great Sea. The people of the Great Sea pass down a legend of a prosperous kingdom with a hidden golden power. Ganon found and stole this power, using it to spread darkness until a boy dressed in green sealed the evil with the Blade of Evil's Bane. The boy became known as the Hero of Time, and passed into legend. One day, the sealed evil began to return, but the Hero of Time did not reappear. The inhabitants of the Great Sea are unsure of the kingdom's fate, but it is clear that this legend is the story of Ocarina of Time.
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 in the children. It is Link's birthday as The Wind Waker opens, and he receives the familiar green tunic and hat. Aryll's present to Link is permission to use her telescope; 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 same 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 thrown from the fortress. 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.
The King of Red Lions gives Link the Wind Waker, a baton able to control the wind and move it in all directions, and instructs Link to sail the Great Sea in search of the three Goddesses' pearls. Link retrieves the pearls and takes them to the three Triangle Islands, causing the Tower of the Gods to rise from the sea. After battling Gohdan in the tower to prove his worth, Link sails into a ring of light and is taken beneath the waters to Hyrule Castle, overrun with enemies and frozen in time. Link descends a hidden staircase and finds the Master Sword, the evil-repelling blade used by the Hero of Time to seal Ganondorf. By removing the sword, Link awakens the castle and all enemies inside. He destroys the enemies and returns to the surface.
With the Master Sword in hand, Link returns to the Forsaken Fortress and joins Tetra and the pirates. He frees the captives and slays the Helmaroc King, but is easily overpowered 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 own power to repel evil. Ganondorf lifts Tetra by the neck, and notices that she is wearing a fragment of the Triforce of Wisdom as a necklace. As he calls her Princess Zelda, two Rito that Link helped while finding the Goddesses' Pearls rescue Link and Tetra, and the dragon Valoo engulfs the fortress in flame.
Link and Tetra sail back to the castle at the bottom of the sea and descend the staircase, where they meet 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 combines a piece of the Triforce of Wisdom with the fragment in Tetra's necklace, causing her to transform into the traditional appearance of Princess Zelda. Link plays the Earth God's Lyric to Medli and the Wind God's Aria to Makar, awakening in them the knowledge that they are Sages of Earth and Wind. Their prayers restore the full power of the Master Sword.
Link goes on a variety of quests to find and decode eight Triforce 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 dwells inside Link, marking him as the Hero of Winds.
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. Ganondorf reveals himself to Link, claiming that Link is the reborn Hero of Time and that fate has allowed him to bring the Triforce together again, just as he had with the Hero of Time. The three Triforces are extracted from Ganondorf, Link, and Zelda and combine to form the complete Triforce. As who ever touches the complete Triforce gets their wish granted, Ganondorf demands that the gods expose Hyrule to the sun once more, under his control. Before he can reach the Triforce, however, King Daphnes