The very start of the prologue covers breifly the story of OoT(which doesn't help if you haven't yet finished it), and then expands on what happened years after, when Ganon re-emerges, and attempts to once again take over Hyrule. This is the point where eveyone in Hyrule was once again expecting a great hero to appear, and save the land from evil. As no hero appeared, the Goddesses had little choice but to flood the entire land, and seal the evil beneath the waves.

Years later, we have The Wind Waker.

Edit: Yes, I'm slow.

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Adopted Bloodsport