The Great Sea is the overworld of The Wind Waker. It is the largest overworld a Zelda game has had to date. Hyrule was flooded by the Goddesses to prevent Ganondorf from taking over the land, and Hyrule became forgotten. The Sky in Skyward Sword is similar in function to this vast sea.
The islands that Link can visit are relatively few compared to the vast sea, The only big city (hub) is Windfall Island. Except for that there aren't any cities, there are small villages on Outset Island and the Ritos occupying Dragon Roost Island. Other than that, Link mainly visits small islands that contain caves, dungeons etc. The sea has also many enemy outposts, monsters and even ghost ships.
The sea is split up into a map, 7x7. On the map there are 49 squares in total. Each square has a landmass on it somewhere, but the islands are very small in comparison to the whole square of water.
In the opening of the game, a story tells the tale of "The Hero of Time" sealing the evil Ganondorf away in the Sacred Realm. After doing so, the Hero of Time left Hyrule, but not before he split the Triforce of Courage into eight shards and scattered them across the land. Eventually Ganondorf escaped his prison and spread evil again, but since the Hero didn't come back, the Goddesses had to flood Hyrule in order to prevent Ganondorf from taking over. They froze him and his armies in time and flooded the place so that they could never be found. Due to this, the citizens had to flee to the mountain tops of Hyrule and start a new life there, and that's how the islands are inhabited.
|Spoiler Alert! This section describes a subject that is sensitive to plot development.|
Link is born on Outset Island. In the beginning on his birthday celebration a pack of pirates arrive at the island trying to save their captain Tetra. When they arrive at the island, they force the Helmaroc King to drop Tetra into the woods, but on behalf of his master Ganondorf, Helmaroc looked for girls with pointy ears and blonde hair (trying to find Zelda) and captured Aryll, Link's younger sister in the process.
Link embarked on an epic quest to save his sister, but to do so he needed to venture to the Forsaken Fortress where the Helmaroc King had been taking the little kidnapped girls. However, when sneaking his way through the fortress, he got thrown out in the sea by Ganondorf. The King of Red Lions found him and saved his life.
After explaining the situation, Link follows the boats lead and journeys to Dragon Roost Island and Forest Haven to retrieve the Goddess Pearls. After doing so, he only needed one more pearl. He found it, and placed them all in the Goddess Statues on the Triangle Islands, awakening the Tower of the Gods. When passing the trials in the Tower, the entity residing in the Tower sent him down to the forgotten land of Hyrule.
Link found the Master Sword and unfroze every monster in the process and Ganondorf's army. Another secret was revealed, Tetra wasn't a pirate, but instead was secretly Princess Zelda and held the Triforce of Wisdom. Down in Hyrule, Link met The King of Hyrule, Daphnes Nohansen Hyrule who turned out to be the King of Red Lions. Link had to retrieve the eight shards of the Triforce of Courage, and he succeeded to do so. Not only that, but he needed to awaken the Earth Sage and Wind Sage to awaken the Master Sword in the process.
He found the Sages' descendants and helped them awaken as Sages. With the Master Sword's full potential back, Link journeyed down to Hyrule again. This time, to finish of Ganondorf and his evil. He fought his way through Ganon's Tower and proceeded to defeat Ganondorf. Daphnes stayed behind and saved Zelda's and Link's life in the process and he told them to find the new land.