Great Flood

The Great Flood is the name often associated with a catastrophic deluge that befell the land of Hyrule many years after the end of Ocarina of Time in the "Adult Timeline". Described in the introduction of The Wind Waker, it occurred when the Ganondorf escaped from his imprisonment in the Sacred Realm and returned to Hyrule, after the departure of the Hero of Time.

Reconstruction
After the Hero of Time defeated Ganon and returned to his own time, as seen in Ocarina of Time, the land of Hyrule began the long process of healing in the wake of Ganondorf's reign of terror. Hyrule Castle was rebuilt near the center of Hyrule on an island in the center of a large lake. For unknown reasons, the Master Sword and the Pedestal of Time were moved to a special chamber in the basement of Hyrule Castle (protected by a giant statue of the Hero of Time himself), where stained glass windows depicted the Seven Sages and the sealing away of Ganon.

Return of the Dark Lord
Many years after the departure of the Hero of Time, the seal of the Seven Sages began to weaken for an unknown reason, and the Dark Lord Ganondorf saw his chance to escape his imprisonment. Using the might of the Triforce of Power, he was able to successfully shatter the seal, reopening the gateway between the worlds and returning to Hyrule. Ganondorf intended to make good on his final threat to the Hero of Time and the Seven Sages that he would return one day to make their descendants pay for his imprisonment. Ganondorf reconstructed his tower headquarters not far away from the new site of Hyrule Castle and attacked Hyrule with his army of dark creatures. The Dark Lord knew the only threat to him lay within the very weapon that defeated him previously, the Master Sword. He sought to render the blade powerless against him and discovered its power was protected by Sages, the Sage of Earth and the Sage of Wind.

Using the power granted to him by the Triforce of Power, Ganondorf entered the Wind Temple and Earth Temple and lay siege to the two Sages. The only consolation for the Sages was that their two special instruments survived the invasion of the temples, and both were passed down to their descendants in turn. There in the depths of the two temples, their spirits would linger on, waiting for their successors to take their rightful place as the new Sages of the Master Sword. With the Master Sword now deactivated and thus powerless against him, Ganondorf continued his attack on the kingdom of Hyrule. The King of Hyrule, Daphnes Nohansen Hyrule, attempted to use the extent of his magic to stop Ganon, but could not overcome the Dark Lord, and left Hyrule's fate to the Goddesses. The people of Hyrule prayed that the Hero of Time would once again come to save them from the very evil he had once helped seal away and thus deliver them once again from evil's grasp.

The Divine Deluge
The Hero of Time did not appear to save Hyrule, having been sent back across the flows of time to his own age. Left with no other choice, the people of Hyrule cried out to the three Golden Goddesses for their help in delivering them from Ganon's evil. Ganondorf was on the verge of completely conquering the land of Hyrule, his troops having even penetrated Hyrule Castle itself. It was then however that the Goddesses answered the peoples' prayers, instructing them to flee to Hyrule's mountaintops in order to escape the apocalypse they were about to unleash upon the land to halt Ganondorf's invasion. King Daphnes Nohansen Hyrule remained behind with his doomed kingdom, though evidenced by Tetra's survival, it is implied that he had Princess Zelda be among her people at the time of the flood. Once the people were safely away, the Goddesses caused a torrential downpour, covering the land and turning the mountaintops into islands.

The goddesses sealed the kingdom within an enchanted air chamber that prevented the water from destroying it. A magical seal was also cast over the Master Sword and the Pedestal of Time that froze the entire land of Hyrule and Ganon's army, freezing them in time and draining them of color. The Golden Goddesses then crafted a great tower that would serve to test the worthiness of any aspiring heroes, in an effort to find one capable of besting Ganon. Only one who conquered the tower's trials would be sent beneath the waves to Hyrule Castle deep to take the up the Master Sword. This tower could only be raised from the bottom of the sea by one possessing the three special Pearls of the Goddesses, one for each Goddess.

The people of Hyrule would then go on to build a new civilization on the surface of the Great Sea and, with the passing of time, largely forget the memory of the old Hyrule that still existed deep beneath the waves.

Aftermath
 Many centuries after the initial flood, Ganondorf broke free of the seal binding Hyrule and returned, intending to reunite the Triforce pieces to reconquer the sunken Hyrule. This caused a new incarnation of Link and Princess Zelda to appear to challenge Ganondorf again, as had their predecessors. After uniting the Triforce, and at the will of the old King, the sacred pieces rise into the air and vanish as the air chamber above them begins to collapse, allowing the Great Sea to pour into Hyrule. After Ganondorf is finally defeated, Hyrule is completely swallowed by water, leaving Link and Princess Zelda to create a new Hyrule above the waves.