Now that Link had all three Pendants of Virtue, he headed toward the Lost Woods to retrieve the Master Sword, the Blade of Evil's Bane that no evil one could touch. The Lost Woods was covered in a mysterious, bewitching fog. Thieves lived here, and every time Link thought he had found the Master Sword, it only turned out to only be a fake. Link searched and searched, until he found a clearing that crawled with friendly forest animals. At the end of the clearing, on top of a platform, Link spotted his goal stuck into a pedestal: the legendary Master Sword.

Using the Book of Mudora, Link read the ancient inscription on the pedestal. It said:

The Hero's triumph on Cataclysm's Eve
Wins three symbols of virtue.
The Master Sword he will then retrieve,
Keeping the Knight's line true.

Taking a deep breath, Link fastened his hands around the Master Sword and pulled. The three Pendants of Virtue floated above his head, and began to flash. Their combined energy gave Link the power to extract the Master Sword from its resting place, and it came loose with a brilliant flash. The fog over the Lost Woods lifted, and sunshine poured through.

At that moment, Sahasrahla contacted Link telepathically. He congratulated Link on his victory, and told him that in order to defeat Agahnim he could not hurt him physically, but would need to deflect his energy back at him using the Master Sword. As Link left the clearing, Princess Zelda contacted Link desperately. Before her last scream was muffled, she managed to tell Link that the soldiers were coming to the Sanctuary to take her away.

Link ran as fast as he could to the Sanctuary, but he got there a second too late. He found the Elder on the ground, wounded. The old man told him that the soldiers had abducted the Princess, and taken her to the castle. He begged Link to find her before the wizard Agahnim could work his magic. Burning with anger, Link ran to the castle and blasted past brainwashed guards using the Master Sword. Finding the tower to Agahnim's chamber blocked by a magical barrier, he used the Master Sword to destroy the barrier.

Inside Agahnim's lair, Link fought past the wizard's best troops, and climbed skyward. When he finally reached the top, he found Agahnim hovering over Princess Zelda, who lay in a trance on a raised platform. Agahnim had been waiting for Link, and told him he wished to make Zelda vanish in front of his very eyes. Horrified, Link watched helplessly as Princess Zelda was spirited away to the Dark World. With an evil laugh, Agahnim taunted Link:

With this, the seal of the seven sages is at last broken. It is only a matter of time before evil power covers this land. After all, the legendary Hero cannot defeat us, the tribe of evil, when we are armed with the Power of Gold.

Laughing again, Agahnim disappeared behind a curtain. Link cut it down and chased after him. Agahnim and Link were now both in the highest room of the castle, and Agahnim promised to completely destroy his foe. Link remembered what Sahasrahla had told him, and didn't hit Agahnim with the Master Sword directly. Instead, as Agahnim teleported around the room, Link waited for him to shoot balls of energy, and Link used the Blade of Evil's Bane to hit them back. Realizing that Link had the power to defeat him, Agahnim stopped fighting. Congratulating Link for his true heroism, Agahnim escaped into the Dark World, and drew Link in with him.