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Ocarina of Time
Link faces Phantom Ganon in the Forest Temple. Phantom Ganon is the boss of the Forest Temple. After Phantom Ganon is defeated Link receives the Forest Medallion. As Phantom Ganon slowly dies, Ganondorf's voice can be heard calling Phantom Ganon a worthless creation and banishes it to the gap between dimensions.
In the manga version of Ocarina of Time Ganondorf calls Phantom Ganon forward and tells him to kill Link before he awaken the Sage of the Forest Saria.
Phantom appears again, but this time as a miniboss. He appears in both the Forsaken Fortress and Ganon's Tower. After defeating Phantom Ganon in the Forsaken Fortress Link receives the Skull Hammer. In Link's second confrontation with him, Phantom Ganon appears in every room of a maze that leads to the light arrows and a rrom after that. After Link receives the light arrows and goes to the next room Phantom Ganon appears for the final time and is killed by a single light arrow.