Before Link left the village, he dropped by a shop to buy supplies. Using thirty rupees that he had found in the Hero's Cave, Link bought a nice Wooden Shield to protect himself from danger.

The Maku Tree had told him to find a "giant root near the lake up north." Link left Horon Village, heading north, and stopped by to visit Impa on the way. Impa told Link that she had seen a gnarled root due north. The land was filled with monsters, so Impa warned the young adventurer to be cautious. Thanking Impa, Link headed north.

After a short journey, Link saw a large lake, and a bridge leading to an island in the middle of this lake. On this island Link found large, gnarled roots, and a keyhole. Link inserted the Gnarled Key, and the ground rumbled as the gnarled wood rose up to reveal an old, dead tree, with an entrance carved into its side. Link ducked to enter the dark tree, emerging in the Gnarled Root Dungeon.

In this dungeon Link encountered Stalfos', skeleton warriors. He found an old wise man, who told him to "return light to unlit torches!" Minecarts took him deeper into the dungeon, where he fought boomerang-throwing, bulldog-faced Moblins. Using a switch to manipulate the tracks, Link was able to ride the minecart to other areas of the dungeon. In a treasure chest sitting next to the tracks, Link found bombs, which would allow him to blow through walls!

Link threw a lit bomb next to the first weak wall he found, and blasted his way into a room filled with razor-sharp moving traps. Link carefully made his way past the traps, and entered a large, empty room. Suddenly, two monsters roared into the room: twin minotaurs, one blue and one red, ferocious half-man, half-bull creatures. They teamed up on Link to throw a boomerang back and forth between each other. But Link dodged their attacks, and valiantly attacked with his sword. Soon they were defeated, and in the basement Link found what they had been guarding: a Seed Satchel filled with twenty Ember Seeds! The Seed Satchel could hold magical Mystical Seeds, and the Ember Seeds, when split open, would shoot forth scorching flame.

Now that Link bore the power of flame, he could take the old man's advice: "return light to unlit torches!" Lighting the torches opened new doors, and Link found the Boss Key, which would let him into the lair of the dungeon's guardian. As Link drew near the boss's lair, Floor Masters, dead hands, rose from the ground, threatening to take Link back to the entrance if they nabbed him. But Link fought them back, and opened the final door.

When Link entered, the door slammed shut behind him. From high above, a fearsome dragon slowly descended to the ground. This dragon, called Aquamentus, had small wings, a single horn on its forehead, and the ability to spit fire from its mouth. It crashed to the ground, and began walking menacingly toward Link. Link dodged its fire, and slashed at its vulnerable head. Suddenly, Aquamentus reared up, and charged! Link jumped away at the last minute, and the dragon slammed with terrifying force into the opposite wall. Flying back, it resumed spitting fire as it walked toward Link. But it could not withstand Link's sword for long, and was defeated.

Link entered the next room, a sacred shrine. On a pedestal was inscribed the symbol of the Triforce, and on this pedestal rested the Fertile Soil, the first essence of nature, which was shaped like a leaf. Seeds scattered across bountiful lands would be nourished in this Fertile Soil. When Link picked up the essence, he felt its power radiating in his hands, and was taken outside the dungeon. In his mind, Link heard a voice speaking to him:

Hwaaah... It's me, the Maku Tree. Some of the Fertile Soil has come to me, too. I already feel stronger. Oh, in my dreams, I saw the Temple of Seasons in a strange land I do not know. There I saw a precious item that will aid you, Link. That is all I can see now... Hohm...hmm...