When Hyrule is flooded by the Gods to protect Hyrule from Ganondorf, it is turned into a vast sea known as the Great Sea. The inhabitants of Hyrule are quickly forced to settle on the mountaintops, and eventually they forget about the land below the sea. The islands scattered around the map become the new home of all life in Hyrule.
In The Legend of Zelda: The Wind Waker and The Legend of Zelda: Phantom Hourglass, Hyrule is completely flooded, and all that remain above the surface are the mountaintops, making up the islands of the Great Sea. It is divided into 49 sections in The Wind Waker each with one island, and into 4 in Phantom Hourglass, each with several islands.
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