Great Flood

This name is conjectural, decided by fans in lieu of an official source.

Great Flood

Games	Described in The Wind Waker
Location	Hyrule
Occurrence	After Era of the Hero of Time Before Era of the Great Sea
Key Characters	Ganon Daphnes Nohansen Hyrule Golden Goddesses
Related	Era without a Hero

The Great Flood occurs hundreds of years after the Adult Ending of Ocarina of Time, after Ganon returns but no hero appears to oppose him. In desperation, the people of Hyrule pray for deliverance. The Golden Goddesses respond by sealing Ganon along with all of Hyrule beneath the newly created Great Sea.

Synopsis

Ganon returns from the Sacred Realm after being sealed by the Hero of Time in Ocarina of Time. With the departure of the hero, the strength of the Seven Sages weakened allowing Ganon to return.

The people of Hyrule prayed that the Hero of Time would return and save the Kingdom however he was nowhere to be seen. Due to the Hero of Time being returned to his own time and not returning. Left hopeless, the current King of Hyrule, Daphnes Nohansen Hyrule, left the fate of the Kingdom to the gods. The Goddesses, in turn, order an evacuation to the mountaintops. Some including, Daphnes Nohansen Hyrule, however, refuse. Hyrule Castle is buried beneath the waves and drained of its color. The mountaintop refuges are transformed into islands.

References

1. ↑ "Long ago, there existed a kingdom where a golden power lay hidden. It was a prosperous land blessed with green forests, tall mountains, and peace." — Prologue, The Wind Waker.
2. ↑ "But one day a man of great evil found the golden power and took it for himself... With its strength at his command, he spread darkness across the kingdom. But then, when all hope had died, and the hour of doom seemed at hand... ...a young boy clothed in green appeared as if from nowhere. Wielding the blade of evil's bane, he sealed the dark one away and gave the land light. This boy, who traveled through time to save the land, was known as the Hero of Time." — Prologue, The Wind Waker.
3. ↑ "Ganondorf, who had once been sealed away, returned from the depths of the earth and covered Hyrule in darkness once again." — Hyrule Historia, pg. 123
4. ↑ "The people hoped that the legendary hero would show up to save them a second time, but… the hero did not appear." — Hyrule Historia, pg. 123
5. ↑ "The boy's tale was passed down through generations until it became legend... But then...a day came when a fell wind began to blow across the kingdom. The great evil that all thought had been forever sealed away by the hero... ...once again crept forth from the depths of the earth, eager to resume its dark designs. The people believed that the Hero of Time would again come to save them. ...But the hero did not appear." — Prologue, The Wind Waker.
6. ↑ "Faced by an onslaught of evil, the people could do nothing but appeal to the gods. In their last hour, as doom drew nigh, they left their future in the hands of fate. What became of that kingdom...? None remain who know. The memory of the kingdom vanished, but its legend survived on the wind's breath." — Prologue, The Wind Waker.
7. ↑ "With no hope of salvation left, King Daphnes Nohansen Hyrule decided to entrust the fate of Hyrule to the Goddesses." — Hyrule Historia, pg. 123
8. ↑ "The Goddesses instructed the chosen people to flee to the mountaintops before drowning both Hyrule and Ganondorf in a massive flood and sealing it at the bottom of the ocean." — Hyrule Historia, pg. 123
9. ↑ "The King was to be sealed along with Hyrule" — Hyrule Historia, pg. 123