Link realized now how Nabooru had become Ganondorf's second-in-command, and why it was said that she was practicing brainwashing in the desert. Link knew he had to defeat the witches and save Nabooru to get the last Medallion, but he couldn't do it as a child. Playing the Prelude of Light, Link warped to the Temple of Time and pulled out the Master Sword.

Now a grown-up again, Link played the Requiem of Spirit to warp to the Desert Colossus. Inside the Spirit Temple, Link now understood the meaning of the riddle concerning the "power of silver." With the Silver Gauntlets equipped, Link easily pushed aside a huge block and delved deeply into the witches' hideout. As he explored, he encountered another Iron Knuckle. This one was easier than the last, because now he had the Master Sword. The door led outside, on the opposite side of the "goddess of the sand" from where Link had picked up the Silver Gauntlets. Inside a chest that dropped down was another treasure: the Mirror Shield. With this shiny shield Link could reflect all kinds of light and energy.

Back inside the dark Spirit Temple, Link found that he could now reflect beams of light to activate sun-shaped switches. With this knowledge, Link moved cobra statues with mirrors on them to reflect light to just the right places, and then use the Mirror Shield to activate a platform. This platform lowered, and Link found himself in front of the largest statue in the Temple, of a woman with a cobra wrapped around her body. Using the Mirror Shield, Link aimed a beam of light into the face of the goddess, and the light's energy was sufficient to break the stone away, exposing a door.

Link made his way to the door, and inside found the two witches in the throne room of another Iron Knuckle. Cackling, the two witches Koume and Kotake promised to teach their outrageous intruder a lesson, and summoned their loyal minion, the Iron Knuckle, to destroy Link on their behalf. The Iron Knuckle rose, paused upon realizing it was defenseless, and produced a double-edged axe out of thin air. Link could tell that this was no ordinary enemy.

When at last the monster's armor fell to the ground in pieces, Link discovered that Nabooru had been inside all along, brainwashed. She dropped to the floor, exhausted after her long ordeal, and moaning, asked where she was. Suddenly the witches appeared again. Kotake noted that Nabooru looked like she was back to normal. Koume mused that although she was just a little girl, Nabooru commanded a lot of respect among the Gerudo, so they should probably make her work for Ganondorf a little while longer by brainwashing her again. Nabooru tried to run, but both witches shot black magic at her, and she disappeared.

The evil sisters disappeared, and Link went through the next door after them. He found himself on a raised platform, with the witches circling above him. Kotake cried gleefully that this kid had come to offer himself as a sacrifice to Ganondorf. Koume vowed to burn him to the bone, and Kotake vowed to freeze him to his soul. With that, the sorceress sisters Twinrova began to attack.

Koume and Kotake shot fire and ice magic at Link, but he reflected it back with the Mirror Shield. Taking careful aim, Link shot Koume with Kotake's reflected ice magic, and shot Kotake with Koume's fire magic. Realizing that they couldn't defeat Link this way, the witches combined in what they called their Double Dynamite Attack. This new foe appeared to be one huge, beautiful sorceress, akin to the Great Fairies Link had encountered. With a sly wink, Twinrova began her attack. She shot alternating bolts of fire and ice. Link figured out that if he absorbed three consecutive bolts of the same kind if energy, he could fire energy back at Twinrova. He did so, and the huge witch dropped to the floor, stunned. Link drew out his sword for the first time, and hacked away. She wasn't done yet, though, and Link continued to fight her. When she was defeated, the witches split up again, promising to really get serious. They didn't realize right away that they were dead. As they argued about their age, they were suddenly surrounded by blue light. They vowed to come back to haunt Link, and disappeared up into the beam of light.

Link went through the portal that appeared, and was taken to the Chamber of Sages. There he met Nabooru again, who said that Link had become a competent swordsman in the past seven years. She admitted that she had messed up badly, and told Link how the old witches had brainwashed her, and how Ganondorf had used her to do his evil will. She promised to fight them as one of the six Sages, and to pay them back for what they did to her. Instead of keeping the promise she made back then, Nabooru gave Link the Medallion of Spirit. As Link left, he heard Nabooru tell him that she would have kept her promise back then, if she had known Link would turn out to be such a handsome man.