Eventually, dark interlopers, later to be called "Twili", attempted to steal the Triforce and establish dominion over the Sacred Realm. In response, the goddesses sent the light spirits Ordona, Faron, Eldin, and Lanayru to seal away their dark magic within the Fused Shadows. The interlopers themselves were banished to the shadowy world of the Twilight Realm (with only the Mirror of Twilight linking the two worlds), where they would become the Twili race. The Mirror was left in the protection of ancient sages.
And then eventually, evil rose once again. A hero would not appear to repel the evil, and in response, the goddesses flooded Hyrule. The citizens were able to flee to the mountaintops, while Ganon and his army were trapped under the sea. The kingdom below was frozen in time to assure Ganon would not utilize his powers to escape, with the Master Sword as its key. The world above would be known as the Great Sea, and the memory of Hyrule was lost with time.