A few years pass, but Link doesn't return - instead, Hyrule begins to be slowly corrupted due to Ganondorf's rule, an unfortunate and unprecedented consequence of Link's opening the Door of Time.

One day, an eerie wind begins to blow from the direction of the Forest Temple, chilling the Kokiri, who have never felt such a breeze. Soon after, the spirits residing in the Temple begin to call for help. Realizing she has to do something, Saria heads to the Temple. She arrives to find the place overflowing with dark energy and monsters. The power is too great and she becomes trapped.

Seven years after opening the Door of Time, Link finds himself in the Temple of Light, facing an ancient Sage named Rauru. Rauru explains to Link that he had been sealed in the Chamber of Sages because before he was too young to become wield the Master Sword. He then tells Link his destiny, as the Hero of Time, to awaken the Sages and destroy Ganondorf. Rauru then directs him to the forest to awaken the first Sage, a girl he's sure Link knows...

Travelling through the Lost Woods towards the Temple, Link is stopped by Mido. Mido doesn't recognize the now grownup Link, even after noticing his Kokirish clothing, and won't let him pass. Attempting to convince him, Link plays Saria's Song, a song she taught only to her friends. Not understanding how the stranger could know Saria, after some thought Mido decides to let Link by nonetheless. However, he makes Link promise, if ever he should see him, to tell the Kokiri boy he resembled who left so long ago that he, Mido, was sorry.

Finally, Link enters the Sacred Forest Meadow, hoping to find Saria. To his great dismay, the stump she used to play her ocarina on lays empty. Just then Sheik appears, reminding Link of his childhood memories and urging him onward. Determined, Link decides to try to contact Saria as he continues to the Forest Temple.

As soon as he can, Link plays Saria's Song, in the hopes to hear she's safe. After a moment, Saria replies, joyous to hear him again but fretful because of her position. Promising to help her, Link sets off to the Forest Temple. Upon arriving at the Temple, Link finds it's exactly how Saria had said it was: completely overrun with Ganondorf's minions. Without hesitation Link rushes in, and after dispelling of the Poe Sisters and Ganon's Phantom, is transported back to the Temple of Light.

There Saria and he finally meet, after seven long years. Unsurprised that Link, unlike the other Kokiri, has grown up, she thanks him for saving her and allowing her to become the Sage of the Forest. Before Link can try to explain, Saria silences him, telling him she understands that their destinies won't allow them to live in the same world. She gives him the Forest Medallion, and promises she will always be there for him, as his friend.

As Link travels to each of the temples, reawakening the Sages and destroying the evil within the temples, Saria, as she did when they were younger, supplies help and advice. When the last temple is renewed and all of the Sages revealed, Link heads to Ganon's Castle for the final fight...