Link, the boy who was entrusted to the Great Deku Tree during the war for the Triforce, was now old enough to blend in with the child-like Kokiri. With the rise of Ganondorf, evil powers had awakened and gained strength. Those sensitive to it, such as the Hylia, could sense this climate of evil permeating Hyrule. Link had been having nightmares lately: while standing in the rain, Link would see a drawbridge lower. A white horse, carrying a woman and a young girl, would come galloping out at top speed. The girl would look at him with panic-stricken eyes, and then Link would turn around to see a man in black armor, riding a black horse, looking down at him with gleeful malice written in his eyes.

Navi found Link in bed, whimpering from the nightmares, and woke the "lazy" boy with a yell. Link hurried to the Deku Tree, but his journey was delayed by Mido, boss of the Kokiri. He wouldn't let Link through until Link had gotten a shield and sword. Link searched until he found the Kokiri Sword, which was supposed to be used only in times of emergency. He finally scrounged up enough rupees to buy a Deku Shield, and only then did Mido begrudgingly let him past. Link found the Deku Tree at the point of death. To test the boy's courage, the Deku Tree told him to enter and break the curse put on him by the thief from the desert. The Deku Tree knew that Link would succeed even though his own life was already doomed.

When Link went inside, he couldn't believe his eyes. The Deku Tree was infected by evil parasites and teeming with monsters. Link had never been in battle before, but he mustered his courage and cut down man-eating plants called Deku Babas, and stabbed at the backside of huge Skulltulas, spiders wearing human skulls. After finding a Fairy Slingshot deep within the Deku Tree's interior, Link could shoot at his enemies from a distance.

Link was able to destroy the parasitic creatures, and at last he found the source of the trouble: a nest of parasitic Gohmas, protected by the one-eyed arachnid Queen Gohma. The giant crablike monster towered over Link with a roar, but Link bravely used the Fairy Slingshot to shoot a Deku Bullet into the monster's one eye. Queen Gohma tried unleashing her offspring, but Link destroyed them as well. When the parasites were finally destroyed, Link was magically transported outside. The Deku Tree told Link about many important things: Ganondorf, the creation of Hyrule, the Triforce, the Sacred Realm. Link's efforts had been successful, but the Deku Tree told Link that his life had been doomed before Link even started. The Great Deku Tree entrusted Link with the Kokiri's Emerald, the Spiritual Stone of Forest, and told him to go to Hyrule Castle to meet the Princess of Destiny. With his dying breath, the Deku Tree entreated Navi to help Link carry out his will. As the Great Deku Tree slowly whithered and turned brown in death, Link and Navi bade their sad farewells.