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. It occurred when the Dark Lord Ganondorf escaped from his imprisonment in the Sacred Realm and returned to Hyrule in a fiery rage. After discovering a way to deactivate the Master Sword’s power by means of disposing of the Sages that safeguarded its power, Ganondorf attacked the land of Hyrule with his army of evil creatures. Because the Hero of Time had left this timeline and no apparent Hero could take up the Master Sword, the kingdom was left nearly helpless against Ganon’s onslaught. Appealing to the Golden Goddesses for their aid in saving them from evil, the people’s prayers were answered when the Goddesses instructed the people to take refuge on the mountaintops of Hyrule and brought down a torrential downpour from the heavens that buried the land of Hyrule beneath a vast ocean that came to be known in time as the Great Sea.

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 eventually rebuilt near the center of Hyrule on an island in the center of what appears to be Lake Hylia (as seen in The Wind Waker), which is fed by a river that is believed by some to be Zora's River itself (since Zora's River was known to feed into Lake Hylia). Hyrule's people began to rebuild their shattered kingdom, and the Hyrulean monarchy was eventually restored with Princess Zelda likely having led the effort to rebuild Hyrule and restore it to its former glory. 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. So Hyrule knew peace for a time, thanks largely to the efforts of the Seven Sages and the Hero of Time, who became legendary in Hylian lore.

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 (possibly because the Master Sword and the Pedestal of Time were taken from their original place near the portal to the Sacred Realm), 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 in a red wrath, intending 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 base 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 an age before, the Blade of Evil's Bane known as 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 crafted two horrible monsters, the giant Poe Jalhalla and the great sand worm Molgera, and ordered them to invade the two temples with his army and dispose of the Sages. Molgera invaded the Wind Temple and settled into the shrine chamber at the heart of the temple after wiping out the Kokiri Sage of Wind, Fado. In turn, Jalhalla invaded the Earth Temple and also settled into the shrine chamber meant for the Earth Sage, wiping out the Zora Sage of Earth, Laruto. 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. Everywhere he went, he rained much death and destruction all throughout the kingdom as the realm descended into darkness. The King of Hyrule, Daphnes Nohansen Hyrule, attempted to use what magic he wielded to stop Ganon, but he was not powerful enough to stop the fiend since Ganondorf possessed the Triforce of Power and had its full strength at his command. 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 as had been hoped, 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 and destruction. Ganondorf was on the verge of completely conquering the land of Hyrule, his troops having even penetrated the majestic 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 it is suspected he sent his descendant, Princess Zelda (seen in one of Hyrule Castle's portraits) away with their people (as evidenced by Tetra's revealed lineage in The Wind Waker). Once the people were safely away, the Goddesses caused a torrential downpour, covering the land and turning the mountaintops into islands.

This was not the complete end of Hyrule however. 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 (now located within Hyrule Castle itself) that froze the entire land of Hyrule and Ganon's army in it right where they stood, freezing them in time and draining them of color. The Golden Goddesses then crafted a great tower that would serve to test any aspiring Heroes, to see if they were worthy of wielding the Blade of Evil's Bane and thus destroy the evil that had haunted the land of Hyrule. Only one who conquered the trials of this tower would be permitted to open a portal that would safely transport him to the remains of Hyrule Castle deep beneath the waves and 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 magical kingdom of 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 to haunt the people above the waves once more, intending to reunite the Triforce pieces and to use the united relic to drain the Great Sea and take over Hyrule as he had in the past. This caused a new incarnation of Link and Princess Zelda to appear to challenge Ganondorf again, as had their predecessors. They rediscover Hyrule's remains at the bottom of the sea and a quest is begun to recharge the Master Sword by Link and the King of Red Lions (the alterego of Daphnes Nohansen Hyrule's spirit). Crossing the sea, Link finds the two new Sages of the Master Sword, a Rito named Medli and a Korok named Makar, and installs them into the Earth Temple and the Wind Temple respectively. After succeeding in restoring the Sages of the Master Sword and returning the power to repel evil to the sword's enchanted blade, Link and the King of Red Lions return to the land of Hyrule beneath the sea, only to discover Zelda has been captured and imprisoned in Ganon's Tower by Ganondorf himself.

Link conquers the trials of the tower and faces Ganondorf atop the roof, where, looking out over the beautiful land of Hyrule, the villain reveals his true reasons for wishing to conquer Hyrule: Ganondorf coveted the lush green fields of Hyrule because the winds there brought life and happiness, whereas he and his people only found death in the winds that blew across the harsh landscape of the Gerudo Desert. Ganondorf then reforms the united Triforce and attempts to wish for the effects of the Great Flood to be undone, therefore exposing Hyrule to the rays of the sun once more with himself as its ruler. However, before he could touch the golden relic, Daphnes Nohansen Hyrule appears and touches it first, instead wishing for Link and Zelda to have a future and for Hyrule to finally be washed away for good, along with Ganondorf and himself. The Triforce pieces rise into the air and vanish as the air chamber above them begins to collapse, allowing the Great Sea to pour into Hyrule. Ganondorf then engages Link and Zelda in a final duel in Hyrule's final moments, but ultimately is defeated when Link plunges the Master Sword into the villain's head, turning him to stone. After a final encounter with the King, during which he instructs them to find a new land the water overtakes the entire world, finally and completely destroying Hyrule as Link and Zelda drift to the surface under the Triforce's magic, where they then set sail across the sea in search of the new land of their own.