NOTES

Sages are the “bridge” between Hyrule and the Sacred Realm. They guard the Master Swords power and protect Hyrule. Each one relates to an element. Light (Hylian, Rauru), Forrest (Kokiri, Saria), Fire (Goron, Darunia), Water (Zora, Ruto), Shadow (Sheikah, Impa), Spirit (Gerudo, Nabooru), and Time (Hylian, Zelda, Leader of the Sages).

End of OOT, adult time line:

The sages seal Ganon in to the Sacred Realm turned Evil Realm.

Zelda uses her power as a sage to send Link back in time to his childhood.

Without a Hero/Link in the adult time line, the Triforce of Courage splits in to eight pieces.

Presumably, the royal family hides these pieces around Hyrule, marking where they are on maps.

The Master Sword was placed back in the pedestal of time within the Temple of Time (which is also the entrance to the sacred realm), sealing the gates to the Sacred-Realm-Turned-Evil-Realm.

After OOT:

Hyrule Castle is rebuilt near the center of Hyrule on an island in the center of Lake Hylia.

It was decided that two new sages should be appointed, the Sages of the Master Sword, to continually pray for the Master Sword to safeguard the power to repel evil that dwells within the enchanted blade.

Two new temples, the Earth and Wind temples, were built for the two new sages, Lauto and Fado.

After a time, for unknown reasons (Temple of Time collapsing?), the Master Sword and Pedestal of Time were moved to a special chamber in Hyrule Castle.

Return of Ganon:

Many years after OOT, the seal of the Seven Sages weakens, possibly due to the Master Sword and Pedestal of Time having been moved from the Temple of Time, and Ganondorf escapes from the Sacred Realm Turned Evil Realm.

Ganondorf, using the power of the Triforce of Power, creates two monsters, Jalhalla for the Earth Temple, and Molgera for the Wind Temple, and order them to dispose of the Sages of the Master Sword.

Without the Master Sword, Ganondorf was free to continue ravaging Hyrule.

The King of Hyrule tried to stop Ganondorf but was not powerful enough.

The people prayed for the return of the Hero of Time but he did not appear.

The Flood:

Without a Hero, the people turned to the Goddesses to save them.

They answered by telling the people of Hyrule to flee to the mountain tops. The King stayed behind in Hyrule and sent Zelda with their people to safety.

The Goddesses created a great storm that flooded Hyrule. The waters rose and created a great ocean, with only the mountain tops to remain as islands.

The Goddesses cast a spell over the country of Hyrule, encasing it within an air chamber that kept the water from destroying the land. - [This is complete speculation on the part of the Wiki I pulled this information from. I found no references that the GODDESSES created a barrier over Hyrule. However, I imagine that only the goddesses have the power to do this:]

The Goddesses set a magical seal over the Master Sword and Pedestal of Time that would keep the land of Hyrule and everyone in it frozen in time. It also served to limit Ganondorf's power, as long as the Master Sword was not pulled from the Pedestal of Time.

Ganondorf was frozen in time below the ocean, along with the King of Hyrule.