The Gnarled Root Dungeon is located in the southeastern part of Holodrum. From Horon Village, head south, then east, and then south again. You'll eventually reach a screen with a large tree stump that serves as the dungeon entrance. Inside, your primary goal is to find the Dungeon Map, the Compass, the Boss Key, and the dungeon item: the Power Bracelet. The Power Bracelet allows you to lift heavy objects like rocks and pots. The dungeon features several rooms with enemies like Gels, Zols, and Moblins. Pay attention to the floor tiles, as some may trigger traps. The mini-boss is a pair of Dodongos; defeat them by feeding them bombs (if you have any, otherwise use your sword after they charge). The final boss is Aquamentus. Use your sword to hit its horn when it's not breathing fire. After defeating Aquamentus, you'll receive the Fertile Soil, your first Essence of Nature, and a Heart Container.
