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Set hundreds of years after the events of Ocarina of Time, The Wind Waker finds the hero Link in a sea scattered with 49 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 in the Great Sea. The people of the Great Sea pass down a legend of a prosperous kingdom with a hidden golden power. An evil man found and stole this power, using it to spread darkness until a young 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. It is clear that this legend is the story of Ocarina of Time, wherein the Hero of Time, Link, fought Ganondorf. When boys on Outset Island come of age, they are customarily dressed in green to pay reverence to the Hero of Time.
Ganondorf, the great evil that all still thought to be sealed away in the Sacred Realm of Hyrule, crept forth, eager to resume his dark designs. As the darkness was spreading over the kingdom, the people hoped that the Hero of Time would once again appear to save them, but the hero did not appear. Ganon's next step was to make another aggressive move for the Triforce. The king, Daphnes Nohansen Hyrule, attempted to stop the fiend, but was not strong enough.
As doom drew nigh, the king and his people prayed to the gods, leaving their kingdom in the hands of fate. The goddesses answered their prayers by instructing those chosen to flee for the mountaintops, before they flooded the land. Ganondorf and his minions were sealed along with Hyrule in an enchanted air chamber at the bottom of the sea, with the Master Sword serving as the key suspending the flow of time within the chamber. Over the centuries, the memory of the kingdom vanished, but its legend survived on the wind's breath.