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- "When the gods heard our pleas, they chose to seal away not only Ganon, but Hyrule itself...and so, with a torrential downpour of rains from the heavens...Our fair kingdom was soon buried beneath the waves, forgotten at the bottom of the ocean."
- — Daphnes Nohansen Hyrule
The Great Flood is an event mentioned in The Legend of Zelda: The Wind Waker. This event occurred hundreds of years before the events of the game and resulted in the total submersion of Hyrule and the formation of the Great Sea.
Many years after Ocarina of Time, the seal on the Sacred Realm began to weaken for an unknown reason, and 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 return to Hyrule in a wrath, meaning to make good on the threat he had 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. As Ganondorf wreaked havoc on Hyrule, the people prayed that the legendary Hero of Time would reappear to save them again as he had done before, but despite their desperate pleas, the Hero of Time did not appear. Hence, they had no choice but to appeal to the gods, hoping that they would save them from Ganondorf.
Seeing that there was no hero to take up the Master Sword and knowing that they could not sit idly by and let Ganondorf take over the land of Hyrule, the gods chose to seal away not only Ganondorf and his minions but Hyrule itself, 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. Therefore, the people who would build a new civilization above the floodwaters were instructed to flee to the mountaintops. Ganondorf's army had reached the gates of Hyrule Castle and was in the process of invading the structure when the gods answered the people's cries. After Hyrule's people had safely escaped, the gods created a great storm that swept the skies over the land of Hyrule, sealing Hyrule and Ganondorf's army under an immense ocean. As the land was drowned beneath the great deluge, 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, Ganondorf, and his army would remain frozen in time, forgotten at the bottom of the vast ocean that now covered Hyrule.
Hyrule's mountaintops became islands on the surface of the newly-created ocean, and the people that had escaped the flood formed new civilizations 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. Only its legend would be remembered. 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, with the islanders hoping for these young men to know courage like that of the Hero himself.
Absence of the Hero of Time
It is stated that, despite the prayers of the people of Hyrule, the Hero of Time did not appear when Ganondorf broke free of his prison in the Sacred Realm, because he had left the land of Hyrule after defeating Ganondorf. It is strongly theorized that the Hero of Time never appeared because after the events of Ocarina of Time, he was transported to Termina, an alternate world of Hyrule, leading up to the events of Majora's Mask. It is possible that he never found his way back to Hyrule after the events of Majora's Mask, thus forcing the Golden Goddesses to seal Hyrule away under the Great Sea.
However, since the legend states that the story of the Hero was passed down for generations until it became legend, it is possible that it was more than a century since Link saved the kingdom by the time of Ganondorf's return.
It was also stated in the Hyrule Historia that the Hero of Time became the Hero's Shade in Twilight Princess, thus heavily hinting that he eventually returned to Hyrule as evidenced by his descendant who is the Link in said game. It is more likely that the Hero of Time merely didn't appear due to going to the Child Timeline (which Twilight Princess is part of).
One possible explanation for the Hero absence, is that by sending the Hero of Time back to relieve his lost childhood, Zelda inadvertently prevented a new hero from appearing when Ganon escaped. There are two possible reasons based on theories about Link's incarnations.
Spirit of the Hero
It has been implied that Link's (as well as Zelda's) various incarnations are in fact reincarnations of the Spirit of the Goddess' Chosen Hero, that appear when Hyrule or the Triforce are threatened by evil. By sending the Hero of Time into the past to relive his childhood, thus creating the child timeline, the cycle of reincarnation was interrupted, preventing a new hero from appearing when Ganon escaped, leading to the Great Flood. By the time of The Wind Waker, the cycle had somehow been restored (possibly with the Hero of Time's death in the child timeline) or the Hero of Winds is part of a new line of reincarnation, unrelated to the original Spirit of the Hero.
Another possibility is based on the idea of the Hero's bloodline, that the various incarnations of Link are part of a shared bloodline (either direct descendants and/or blood relatives) much like the Royal Family of Hyrule. Given that the Hero of Time was an orphan, it is possible he was the only surviving member of the Hero's bloodline (spelling the end of his bloodline in the Adult Timeline). Another is that loss of the Hero of Time's potential offspring caused his bloodline to diminish in the Adult Timeline to the point it prevented a new incarnation of Link from appearing when Ganon escaped resulting in the events of the Great Flood. This means the Hero of Winds is either part of a new bloodline or that part of the Hero's bloodline survived (for example, Link, his Grandmother, and Aryll may be distant relatives of the Hero of Time).
Events in The Legend of Zelda series
|Creation of Hyrule · Great Cataclysm · Great Flood · Peace Agreement · Shipwreck|
|Great War of Ikana · Hyrulean Civil War · Imprisoning War · War of the Bound Chest|
|Carnival of Time · Hyrule Festival · Korok Ceremony · Picori Festival · Picori Festival Tournament · Wing Ceremony|
|Autumn · Spring · Summer · Winter|
|Endless Day · Endless Night · Graduation Ceremony · Horde Battle · Jam Session · Lunar Phases · Oasis Flight · Restoration Ceremony|
|Bad Uncle Rupee's Ashen Rupeeland · Destruction of Termina · Game Over|