The story of Zelda: The Wind Waker is placed 100 years after Ocarina of Time, and a new Link has been born in a Hyrule that was flooded by a deluge. Most of the kingdom is underwater, but the the highest peaks are visible, and in these new islands people live as well as monsters. A few islands have temples that once were inhabited by the sages, but when the last sages died the new world went into chaos. More monsters started to appear across the Great Sea, even in islands occupied only by Hylians.
In the verge of the new catastrophe, the new Link is called to duty when his sister Aryll is captured by the Helmarock King and it's his duty to go and save her. However, when Link is about to save Aryll, he is suddenly blasted away by Gannondorf and thrown into the ocean, only to be saved by a mysterious talking ship who says he is "The King of Red Lions". The King starts to explaining you what is happening--the evil king Ganon is out his prison and creating chaos around the world, and it is your job as the chosen one to stop him at any cost.
The story is quite similar as many Zelda games, where there is an endless cycle of good and evil, but that doesn't mean that the game is just another Zelda, because there are a few improvements in the story and basically Wind Waker is a sequel to Ocarina of Time, even if it don't show many elements of Ocarina of Time, such as the Ocarina. The given score to the story is a perfect five.