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When Link first arrives at the Forsaken Fortress, he loses his sword and must "sneak" around the fortress using barrels and defeating the searchlight controllers with their own weapons (or weapons found in jars). Despite regaining his sword and finding his sister, The Helmaroc King swoops in and throws Link far out to sea.
Eventually, Link has gained enough experience that he can go back and save his sister. Unlike the previous attempt, he actually succeeds and comes into a confrontation with Ganondorf, who watched the entire thing from a small room on top of the fortress. He explains why the Master Sword was sealed away and that, in is current state, cannot repel evil. Tetra manages to sneak into the room and stun Ganondorf momentarily, until he grabs her and reveals the Triforce on her hand. Members of the Rito tribe manage to swoop in and save Link and Tetra, Ganondorf confused, and Valoo appears outside the window and breathes onto the room, burning it to a crisp.