According to Link's map, the next maiden was being held in the Skull Woods, the Dark World's evil incarnation of the Lost Woods in the Light World. Link couldn't find an entrance into the Skull Woods no matter how hard he looked. He remembered what the last maiden had told him, that other magical portals between the worlds existed. Using the Magic Mirror, Link warped to the Light World, and explored around the entrance to the Lost Woods and Kakariko Village. He followed a path north from Kakariko Village, through the Lost Woods, and south again towards Kakariko. Pounding down some stakes that were in his way, Link found some bushes and a suspicious-looking rock. Lifting the rock, Link found another portal into the Dark World.

Throwing the rock aside, Link entered the teleporter and warped to the entrance of the Skull Woods in the Dark World. Fog drifted through the dead trees, and huge rocks that looked like skulls gaped out of the lifeless dirt. As Link walked along, wondering where the imprisoned maiden could be, he suddenly fell into a hole in the ground. He found himself in a crypt overgrown with vines, facing mummy-like Gibdos. Their wrappings protected them from Link's repeated blows. In a large chest Link picked up a magical artifact: the Fire Rod. This magic-consuming shaft could shoot fire at Link's enemies and at unlighted lamps.

By now Link had found several exits to the outside through the mouths of some of the skull rocks. Link kept exploring, until he found what looked like a large insect crafted from stone. Link was sure that this would lead to the maiden, but he didn't know how to get inside. Then he noticed that the sculpture was really the bones of what was once a huge monster. Using the fire rod to burn it down, he was now inside the final lair. Before long he met up with the monster guardian: Mothula. This insectoid flew above Link, raining down beams of fire energy. Stepping carefully on the slippery floor, Link shot his fire rod at the moth, and struck with his sword for good measure. After a long fight, Mothula was defeated.

Link picked up the crystal, and the maiden told him the prophecy of the Great Cataclysm. She told him that, since he was in the blood-line of the knights, he must rescue Zelda without fail.