You have defeated Ganon and locked him in the Sacred Realm. After Zelda sends you back in time, you peacefully reside in Kakariko Village. (Navi somehow came back to Link, don't ask xD) Word spreads of a new evil that dwells deep in a hidden and unexplored part of the Lost Woods. You decide to try and kill it, but it is FAR more powerful than Ganondorf ever was.