If you don't know, that game is pretty much after what happened in the GC version of Zelda, "The wind waker". In that version you face Gannon as your last boss and I suspect that he dies or disappears forever after that, but I havn't quite beaten him yet.
I known this from the start when in the instruction booklet I read the story (If you have read the story part, usually you never do read the story part of the instruction booklet) and also at the start when it had the storyboard with the cut out figures. In the story board it said something about beating this evil guy, yes that was Gannon. The whole storyboard at the start was pretty much the events of "The Wind Waker" version.