Great Flood
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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 what many fans have come to call the "Adult Timeline". It occurred when the Dark Lord Ganondorf, the King of Evil who had reigned over the land of Hyrule as a tyrannical usurper king for seven dark years until the reappearance of the Hero of Time and his subsequent defeat at the Hero's hands, escaped from his exile in the tainted 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 safeguard its power, Ganondorf assumed his bestial form of the Dark Beast Ganon and attacked the land of Hyrule with his army of evil creatures. With the Hero of Time no longer in that branch of Hyrule’s history due to his departure back to his own age and no apparent Hero to 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. This was not the complete end of Hyrule however, as Hyrule was sealed 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 everyone in it right where they stood, freezing them in time and draining them of color, primarily Ganondorf and his army. 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.
The Legend of the Hero of Time
Ancient legends in the land of Hyrule spoke of a legendary Golden Power, the Triforce, that resided in the magical Sacred Realm and had the power to grant the wishes of one who mastered it in its entirety. One day long ago, a man of great evil named Ganondorf, of the Gerudo tribe, schemed to enter this magical realm and lay claim to the Triforce in order to become the true master of the world. With the unwitting assistance of a young boy named Link (who would grow up to become the Hero of Time) and Hyrule's Princess Zelda, Ganondorf was able to enter the Sacred Realm through much cunning and deceit. However, because his heart was not in balance, the Triforce separated upon being touched by Ganondorf's tainted hands, leaving him with only the Triforce of Power and transforming the Sacred Realm into a corrupt world of evil and despair. The Triforce of Wisdom was then bestowed upon Princess Zelda and the Triforce of Courage upon the Hero of Time respectively. The Hero of Time was put into an enchanted slumber for seven years until he matured enough to properly handle the Blade of Evil's Bane, the Master Sword, which he had removed from the Pedestal of Time. Meanwhile, Zelda went into hiding (disguised as a Sheikah warrior known as Sheik) for the seven dark years of Ganondorf's evil reign over the kingdom as the Usurper King of Hyrule, awaiting the time when Link would reappear and they could overthrow Ganondorf together.
Sure enough, Link returned seven years later from the Sacred Realm and came in search of the mythical Seven Sages who were said to have the power to bind Ganondorf and return the light of peace to Hyrule. Through much toil and trouble, the Hero of Time braved the many evils Ganondorf had cast upon the realm and sought out each of the major temples throughout Hyrule and, on the instructions of Rauru the Sage of Light, awakened each of the Seven Sages, who curiously turned out to be figures he himself had befriended in his childhood (Saria the Sage of Forest, Darunia the Sage of Fire, Ruto the Sage of Water, Impa the Sage of Shadow, and Nabooru the Sage of Spirit). After each of the Sages had been awakened, Princess Zelda revealed herself to be the seventh Sage and Leader of the Sages as well as revealing that she and Link both contained the other two pieces of the Triforce Ganondorf had failed to capture. Ganondorf soon captured Zelda however and hoped to use her as bait to lure the Hero of Time to his tower keep at the top of his castle in order to steal the Triforce of Courage back from him. Link followed to the fiend's castle and, with the assistance of the remaining Sages, entered Ganon's Castle and fought his way to Ganondorf's throne room atop Ganon's Tower. Here the Hero of Time confronted the King of Evil in an epic battle that ended with Ganondorf collapsing to the ground seemingly dead and Zelda released from her prison. Ganondorf then attempted to crush the two in the ruin of the tower however when he began to bring down his own castle around them. The pair escaped in time however, only to see Ganondorf emerge from the rubble and transform into the Dark Beast Ganon. The Hero of Time then fought Ganon in hand to hand combat and defeated him with the might of the Master Sword, allowing the Sages the time they needed to bind him and throw him back into the tainted Sacred Realm before sealing the portal between the worlds. Ganondorf screamed in rage that as long as the Triforce of Power was in his hand, he would return one day to exterminate the descendants of the Hero of Time and the Sages to make them pay for his imprisonment. Princess Zelda then used her power as a Sage to send the Hero of Time back to his own age in order to regain his lost childhood. Upon his departure, the Triforce of Courage split apart into eight shards and scattered across the land to be found again one day by another Hero that would have need of its power. The Master Sword was also left in the Hero's wake, being returned to its pedestal in turn. With this act, the Hero of Time vanished from this branch of Hyrule's history, leaving only his legend behind.
Reconstruction
The land of Hyrule began the long process of healing in the wake of Ganondorf's reign of terror over the kingdom that left it a sad ruin of its former self. 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. As time would go by, it was eventually decided that a new set of Sages would safeguard the Master Sword's power by continuously praying to the Goddesses for its power to forever remain within its enchanted blade. As such, two new temples were constructed for the so-called "Sages of the Master Sword", with the Wind Temple built inside one of the mountains to the north and the Earth Temple built within another large mountain to the south. The temples were each built with two different entrances, one at ground level and the other residing at the mountain's summit. Three new instruments were also created to carry the Sages' prayers to the Goddesses: a harp that would be held by the Earth Sage, a violin that would be held by the Wind Sage, and a magical conductor's baton known as the Wind Waker that would be used by the sitting ruler of Hyrule to conduct the other two in unison. For unknown reasons (perhaps because the Temple of Time took structural damage during Ganondorf's reign and eventually collapsed), the Master Sword and the Pedestal of Time were moved to a special chamber in the basement of Hyrule Castle, 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.