Link hookshot a branch and entered the Forest Temple. The temple was permeated with a sense of quiet, ominous ill will. Inside he found an enchanted elevator and four torches that controlled it. Four Poe sisters suddenly appeared, and stole the flames away. Joelle took the orange flame, Beth took the blue flame, Amy took the green flame, and Meg took the purple flame. The elevator lowered, keeping Link from reaching the lower level of the temple. Link searched through the temple, looking for the Poe sisters, fighting off Stalfos, and avoiding Wallmasters. Finding a Fairy Bow, Link shot arrows into paintings of the Poe sisters. The Poe sisters had been hiding in these paintings, and Link was able to reclaim three of the four flames.

The last Poe sister, Meg, used her magic to make replicas of herself circle around Link. Link knew which of the four was real, and eventually the last flame was recovered. Link went down to the lower level, where he came upon a room with paintings on the walls. When he turned around to leave, the exit was blocked off, and behind him appeared the Evil Spirit from Beyond, Phantom Ganon. Phantom Ganon and a copy rode in and out of the paintings, and Link aimed carefully and shot arrows at the real Phantom. Finally Ganondorf's Phantom ditched its horse and floated in the air, throwing magic spells at Link. Link hit them back with the the Master Sword, and the ball of magic flew back and forth between the two faster and faster. After a long battle, Link defeated Phantom Ganon. Suddenly Ganondorf's voice boomed through the room:

Hey kid, you did quite well... It looks like you may be gaining some slight skill... But you have defeated only my phantom... When you fight the real me, it won't be so easy! What a worthless creation that ghost was! I will banish it to the gap between dimensions!!

Link warped to the Chamber of Sages, where he witnessed Saria's awakening as the Sage of Forest. Saria had known Link would return some day, but she recognized that it was fate that they could not live in the same world together. Saria gave him the Forest Medallion, and Link was transported in front of the Deku Tree. Since the curse on the Forest Temple had been broken, life could now flourish. The Deku Tree sprout, imbued with all the wisdom of the old Deku Tree, popped up and told Link the story of how he had come to live with the Kokiri.

Some time ago, before the King of Hyrule unified this country, there was a fierce war in our world. One day, to escape from the fires of the war, a Hylian mother and her baby boy entered this forbidden forest. The mother was gravely injured... Her only choice was to entrust the child to the Deku Tree, the guardian spirit of the forest. The Deku Tree could sense that this was a child of destiny, whose fate would affect the entire world, so he took him into the forest. After the mother passed away, the baby was raised as a Kokiri. And now, finally, the day of destiny has come!

Link finally discovered that he was a Hylian, and that this was why he had grown old while the rest of the Kokiri had stayed young.