Adult Timeline
Link defeats Ganon as an adult but vanishes back to childhood — and with no hero left, the gods drown Hyrule to contain Ganon's return.
Fork point: Ocarina of Time
Diverges from Shared Trunk (Before the Split)
The Story Arc
Here the Hero of Time wins — and then disappears, sent back to his own era, leaving the adult world without its hero. When Ganon eventually escapes his seal, no one can stop him, and the gods make a terrible choice: they flood Hyrule, sealing kingdom and King of Evil alike beneath a vast ocean.
The Wind Waker opens centuries later on that Great Sea, where a new Link — no chosen bloodline, just a boy from Outset Island — sails to save his sister and inherits the hero's title on merit. Phantom Hourglass picks up literally the next day. Spirit Tracks closes the branch roughly a century on, in New Hyrule, a country founded by Tetra's pirates far from the drowned original.
Games, in chronological order
The Wind Waker
Adult Link defeated Ganon but never returned to warn anyone of the coming danger; when Ganon later resurfaces, the gods flood Hyrule to contain him. Centuries later, a new Link sails the Great Sea to rescue his sister and uncover his kingdom's sunken past.
Phantom Hourglass
A direct sequel picking up the next day after Wind Waker, Link chases the ghost ship that abducted Tetra into the spirit world of the Ocean King, using the DS touch screen to steer his boat and solve puzzles.
Spirit Tracks
Roughly a century after Phantom Hourglass, in New Hyrule founded by Tetra's descendants, Link and the ghost of Princess Zelda restore the Spirit Tracks binding the Demon King Malladus, closing out the Adult Timeline.