The Wind Waker

TThe mountaintops of flooded Hyrule are now the islands of the Great Sea. On Outset Island boys dress in green when they come of age, in memory of the Hero of Time.

On Link's birthday a giant bird snatches his little sister Aryll. Link, who Hyrule Historia says is not descended from the Hero of Time, joins the pirate captain Tetra and her crew to reach the Forsaken Fortress. A talking boat, the King of Red Lions, guides him across the sea. Ganondorf has escaped the Sages' seal and is having girls with pointed ears kidnapped.

Ocarina of Time's peoples survive in new forms. The Zora have become the Rito of Dragon Roost Island. The Kokiri have become the leaf-masked Koroks of the Forest Haven. Hyrule Castle waits under the sea with the Master Sword. Tetra is revealed partway through to be heir to Hyrule's royal line.

It begins the adult timeline. Phantom Hourglass follows directly and Spirit Tracks a century later.