Great Flood

The Great Flood was a war of apocalyptic measures many years after the Imprisoning War, in the timeline set during the imprisonment of Ganon. The war would result in Hyrule being sealed beneath the Great Sea inside an enchanted air chamber, along with Ganondorf and his army.

The Great Flood is discussed in the opening of The Legend of Zelda: The Wind Waker as well as within the game itself.

The Legend of the Hero of Time
Long ago, a man of great evil, the Dark Lord Ganondorf of the Gerudo tribe, schemed to enter the Sacred Realm of legend and to take the all-powerful relic known as the Triforce that dwelt within the Sacred Realm for his own evil ends. Through manipulation and treachery, the Dark Lord succeeded in entering the Golden Land of the Triforce by means of manipulating the Princess of Hyrule, Princess Zelda, and a heroic young boy from the forest named Link that sought to keep Ganondorf from his goal. After the boy had collected the three Spiritual Stones from Hyrule's various races as well as the Ocarina of Time from Princess Zelda, he was able to open the barrier between Hyrule and the Sacred Realm within the ancient Temple of Time, the Door of Time, and discovered the legendary Blade of Evil's Bane, the Master Sword, just beyond the Door of Time. The boy removed the sword from the Pedestal of Time and opened the way to the Sacred Realm, but he was placed in suspended animation for seven years until he was old enough to properly handle the Master Sword and claim the mantle of the Hero of Time. In an event that came to be known in history as the Great Cataclysm, Ganondorf was able to enter the Sacred Realm and laid his blood-stained hands on the sacred Triforce, but because his heart was not in balance, the Triforce split into its three component pieces, leaving Ganondorf with only the Triforce of Power. The other two sacred triangles, the Triforce of Wisdom and the Triforce of Courage, were transported to Princess Zelda and the newly-minted Hero of Time respectively.

After ruling Hyrule for seven dark years, Ganondorf was confronted with the return of the now-grown up Hero of Time, who now wielded the Master Sword with ease. The Hero of Time cast down Ganondorf's evil monsters throughout Hyrule and awakened all of the legendary Seven Sages, who then fought alongside the Hero of Time to defeat Ganondorf and restore peace to the land of Hyrule. After all of the Sages had been awakened, Princess Zelda revealed herself to be the seventh Sage and Leader of the Sages to the Hero of Time, but Ganondorf captured her and took her to his tower, Ganon's Tower. Using her as bait, he hoped to lure the Hero of Time to his lair in order to reassemble the one true Triforce and reclaim its full power. The Hero of Time did indeed follow to the fiend's tower, and entered with the help of the remaining Sages. The Hero worked his way up through the dark castle, all the way to the top of the castle's keep, Ganon's Tower. At the top, he found Ganondorf and the imprisoned Princess Zelda awaiting him. Ganondorf then fought a great battle with the Hero of Time atop the tower, but he was ultimately bested by the Hero of Time and the Master Sword he wielded. Zelda was released, but the tower began to crumble as Ganondorf attempted to crush the two in the collapsing structure's wake using his last breath. The Hero of Time escaped the castle with Princess Zelda just in time before the structure collapsed entirely, leaving only a pile of rubble. Ganondorf, still in possession of the Triforce of Power, exploded out of the rubble of his own castle, seemingly immortal with it in his possession. Using the sacred triangle's full power, he transformed himself into the monstrous Dark Beast Ganon, a boar-like terror that rained death and destruction wherever he went. The Hero of Time once again defeated Ganon with the Master Sword's power however, and the Seven Sages opened the doorway to the now-tainted Sacred Realm (the Dark World) and sent Ganon through it, sealing the gateway in the process. As he drifted away into the void, Ganondorf screamed to his captivators that he would return and exterminate their descendants one day when the seal was broken since the Triforce of Power was still in his possession. Following Ganondorf's sealing in the Dark World, Princess Zelda used the Ocarina of Time to send the Hero of Time back to his childhood to regain his lost seven years, leaving only his legend behind. Upon his departure, the Master Sword was returned to the Pedestal of Time and the Triforce of Courage was split into eight shards that scattered across Hyrule, only to be found one day by another Hero who would have need of its power. This conflict, one of the most famous in Hyrulean history, came to be known as the Imprisoning War.

Reconstruction
Following the Hero of Time's departure through the flows of time back to his childhood, the Kingdom of Hyrule began the long process of healing and reconstruction in the wake of Ganondorf's evil reign. Hyrule Castle was rebuilt near the center of Hyrule with a large moat surrounding it that was fed by Zora's River. The Master Sword, left behind when the Hero of Time returned to his childhood, was returned to the Pedestal of Time and remained there for a certain number of years. As was the case with its counterpart in the other branch of Hyrule's history, the Temple of Time likely fell into ruin as well over the following years, having taken structural damage from the years of Ganondorf's reign, and eventually collapsed, as evidenced by the ruins seen near Hyrule Castle where the Temple of Time would have been. In any event, it was eventually decided that the Master Sword and the Pedestal of Time, the two surviving relics of the Temple of Time, be accorded a special place of honor in a secret room in Hyrule Castle's basement following the Temple of Time's demise. The chamber was decorated with stained-glass windows of the Seven Sages awakened by the Hero of Time as well as both the Triforce and Ganon. This hidden chamber was sealed by a mighty stone statue of the Hero of Time that stood tall in the halls of Hyrule Castle. The land finally began to return to a state of peace and prosperity for a good many years following the Imprisoning War's end, and all seemed well thanks to the efforts of the Hero of Time and the Seven Sages. It was then decided that to safeguard the Master Sword's power to repel evil and to make sure that it would always be ready should Ganondorf ever return from his exile in the Sacred Realm, two new temples would be constructed for two new Sages, the Sages of the Master Sword. These two new Sages, the Sage of Earth and the Sage of Wind, would be primarily responsible for praying to the Goddesses that the power to repel evil would forever remain within the enchanted blade of the Master Sword. That power would always be present as long as these two new Sages continued their prayers to the Goddesses. Hence, the two new temples, the Earth Temple and the Wind Temple, were constructed inside two very large mountains in the south and north of Hyrule respectively. Three special instruments were then crafted for the purpose of carrying the Sages' prayers to the Goddesses: a harp to be used by the Sage of Earth, a violin to be used by the Sage of Wind, and a magical conductor's baton that would lead the other two instruments known as the Wind Waker, which would be wielded by the King of Hyrule. So Hyrule was finally restored to its former beauty, and peace reigned for many years.

Return of the Dark Lord
Many years (possibly centuries) following the Imprisoning War's end, the seal on the Dark World began to weaken for an unknown reason (possibly because the Master Sword and the Pedestal of Time had been taken from their original place near the portal to the Sacred Realm), and the Dark Lord Ganondorf saw his opportunity to finally break free of his prison. Using the might of the Triforce of Power, Ganondorf was able to fully break the seal on the Dark World and returned to Hyrule in a red wrath, meaning to make good on the threat he'd made many years earlier to the Hero of Time and the Seven Sages that he would make their descendants as well as all of Hyrule pay for his imprisonment.

The Dark Lord used the might of the Triforce of Power to reconstruct his tower not far away from the new site of Hyrule Castle. From here he launched the beginning phase of an invasion to conquer the land of Hyrule. Ganondorf soon learned that the Master Sword's power was safeguarded by two new Sages, the Sage of Earth and the Sage of Wind, and knew that the only thing that could truly harm him was the Master Sword itself, the evil-destroying blade that had defeated him during the Imprisoning War. Thus, he sought a way to deactivate the sword's true power and discovered that he need only root out these two Sages to remove the power to repel evil from the sword's blade. To this end, he used the Triforce of Power to craft two horrible monsters, a giant Poe named Jalhalla and a great sand worm named Molgera. He then ordered Jalhalla to take a legion of his troops and invade the Earth Temple to the south and Molgera to take another legion of troops to invade the Wind Temple to the north. Ganondorf ordered the two beasts to destroy the Sages of the Master Sword and to inhabit the temples to prevent new Sages from being installed. Obeying their master's orders, the two monstrosities left for their destinations, each with a platoon of Ganondorf's monsters in tow.

Jalhalla arrived at the Earth Temple with Ganondorf's soldiers, and they quickly overtook the temple, killing all in their path. As the troops invaded the temple's chambers, Jalhalla moved to the heart of the temple and found the current Sage of Earth, a female Zora named Laruto (possibly a descendant of Princess Ruto, the Sage of Water during the Imprisoning War), praying to the Goddesses for the Master Sword to always have the power to repel evil at the temple's main shrine made for the Sage's prayers. The giant Poe then assaulted Laruto and murdered her, stealing her soul and taking control of the temple's shrine. Laruto's harp, the only thing to escape the assault on the Earth Temple, was passed on to her family and down her family line following these events. Meanwhile, Molgera arrived at the Wind Temple inside one of Hyrule's northern mountains along with another legion of Ganondorf's troops, and the army quickly overran the temple, flooding its halls with evil creatures. Molgera proceeded into the temple's depths, to the deepest chamber of the entire structure. Finally, the beast arrived at a large, cylindrical chamber half-filled with sand that surrounded the temple's main shrine down in the sandy pit. And there, also praying to the Goddesses for the Master Sword's power, was a Kokiri named Fado (possibly a descendant of Saria, the Sage of Forest during the Imprisoning War), the current Sage of Wind. The great worm overwhelmed the small Kokiri Sage and murdered him, stealing his soul and taking up residence in the shrine chamber of the temple. The only thing to survive the invasion of the Wind Temple was Fado's magical violin, which was passed on to his family and down their line thereafter.

Once this was done, Ganondorf assumed his Dark Beast form of Ganon and attacked the Kingdom of Hyrule head-on, leading the bulk of his army in an invasion of the Kingdom and raining death and destruction all around him. As he wreaked havoc on the Kingdom, the people prayed that the legendary Hero of Time would reappear to save them again from Ganon as he had done during the Imprisoning War, but despite their desperate pleas, the Hero of Time was unable to answer their cries for help due to the fact that he and his descendants were no longer in that branch of Hyrule's history as a result of Princess Zelda sending the Hero of Time back to his childhood at the conclusion of the Imprisoning War. Hence, they had no choice but to appeal to the Goddesses for their help in saving them from destruction at the hands of Ganon.

The Divine Deluge
The desperate cries of the people of Hyrule eventually reached the ears of the Golden Goddesses Din, Nayru, and Farore. Seeing that there was no Hero to take up the Master Sword against Ganon and knowing that they could not sit idly by and let Ganon once again take over the land of Hyrule, the Goddesses instructed the people to take refuge on Hyrule's mountaintops. They had decided upon sealing not only Ganon but Hyrule itself away, but knew that to seal Hyrule's people away with the Kingdom would only grant the King of Evil's wish for the destruction of the land. Ganon's army had reached the gates of Hyrule Castle and were in the process of invading the structure when the Goddesses answered the peoples' cries. After Hyrule's people were safely away, the Goddesses created a great storm that swept the skies over the land of Hyrule and brought down never-ending rains that began to flood the kingdom in an event that would come to be known as the "Great Flood." The Zoras, being expert swimmers, saved many from the flood as the land was overtaken by water and helped them escape to the mountaintops as well. As the land was drowned beneath the great deluge of rainwater, an enchanted air chamber was cast over the entire kingdom, preventing the water from destroying the land and merely sealing it beneath the large body of water that was formed. At the same time, the entire land and everyone still in it were frozen right where they stood, kept in stasis by a seal cast upon the Master Sword and the Pedestal of Time. As long as the Master Sword was not removed from the Pedestal of Time, Hyrule, Ganon and his army would remain frozen in time, forgotten at the bottom of the vast ocean that now covered Hyrule and left it a forgotten memory at the bottom of the sea. Hyrule's mountaintops became as islands on the surface of the newly-created ocean, and the people that had escaped the deluge formed a new country upon the surface of the sea, eventually forgetting about the ancient land of Hyrule that still existed at the bottom of the ocean and the evil that had been sealed away with it. The Goddesses crafted an immense tower to test the courage of possible Heroes that wished to wield the Master Sword and ultimately destroy the evil that haunted Hyrule one day and sealed the tower at the bottom of the sea as well. They each created a pearl and gifted them to Hyrule's surviving races, the pearls being the keys that would, when placed in the proper places, raise the Tower of the Gods from the bottom of the sea and open the way to the Master Sword at the bottom of the ocean. The people created a new civilization on the surface of the sea and its islands (Hyrule's former mountaintops), and with the passing of time, the memory of the land of Hyrule was all but forgotten, with only its legend surviving on the wind's breath. On Outset Island, it became customary to garb young boys in green when they came of age as a homage to the Hero of Legend (the Hero of Time), with the islanders hoping for these young men to know courage like that of the Hero of Time himself.