Great Flood

The Great flood, as described in The Wind Waker, was the work of "the gods." This event occured sometime after the happenings of Ocarina of Time in response to Ganon's return. Hyrule and Ganon were sealed under the water, and the survivors found refuge on the high mountain tops, which became islands. The flooded kingdom later became known as the Great Sea. After many generations, Hyrule was all but forgotten.

At the end of The Wind Waker, the king of Hyrule, Daphnes Nohansen Hyrule, tells Link and Princess Zelda to go and find a new land. Many fans believe, this new land is the Hyrule that is featured in later games in the timeline. Another theory arose from a statement by the Deku Tree, "Forests have great power, they can change one tiny island into a larger island. Soon, a day will come when all islands are one, connected by earth and grove."

There are many theories, but at this time, it is still unclear which one of them is correct.