Link ran out of the Temple of Time, and took the path that led to Ganon's Castle. Ruin and chaos had taken the place of the beauty and order that had prevailed here seven years ago. The Castle itself floated above a lava-filled pit, and Link couldn't figure out how to get to the entrance. Suddenly, Rauru contacted Link, telling him that the six Sages would gather their power to create a bridge to the castle where Ganondorf dwelled. The castle's keep, which was known as Ganon's Tower, was protected by six evil barriers. Rauru instructed Link to bring down the six barriers and save Princess Zelda.

A magical bridge, in appearance like iridescent crystal, appeared, spanning the gap over the pit to the entrance of Ganon's Castle. Inside, Link saw a magical barrier in front of the entrance to Ganon's Tower. The magical barrier drew its energy from barriers of forest, water, shadow, fire, light, and spirit. Link penetrated the forest obstacle course to find a barrier at the end. A Light Arrow was sufficient to dispell the Forest Barrier, and Saria appeared to him and told him to hurry. Link did the same thing for the Water Barrier. In the Shadow Obstacle course, Link uncovered a chest containing the Golden Gauntlets, which allowed him to lift up huge pillars of stone.

Link used the Golden Gauntlets to pass the test of fire and dispell the Fire Barrier. A stone pillar blocked the entrance to the obstacle course of Light, and Link lifted it up and threw it into the air behind him. It hit the barrier and shattered into pieces. After the Light and Spirit Barriers were dispelled, the magical barrier disappeared. Link was tempted to rush right into Ganon's Tower, but he went back outside first. Nearby was another huge pillar, and using the Golden Gauntlets, Link exposed the dwelling place of the Great Fairy of Courage, who enhanced his defensive power.

Back in Ganon's Tower, Link could hear the sound of an organ being played far above. He climbed countless stairs, fighting a pair of Dinalfos' in one room, and a pair of Stalfos' in another. Climbing further, Link found a room with two Iron Knuckles: one shone white like silver and the other was iron black. Link woke them up and fought both of them at the same time. The next set of stairs led Link into a room with a tall platform, which extended higher than the ceiling. After a final set of stairs, Link was at a big door, and unlocked it with the key he had won from the Stalfos'.

Ganondorf was playing an organ, and had his back turned away from the door. Zelda floated in the air, still trapped in the crystal. The Triforce symbol shimmered golden on Zelda and Link's hands, and Ganondorf, still playing the organ with his back turned, said,

The Triforce parts are resonating... They are combining into one again... The two Triforce parts that I could not capture on that day seven years ago... I didn't expect they would be hidden within you two!

Ganondorf let fly an evil laugh, because all the Triforces pieces had gathered in one place. Spinning around, Ganondorf claimed that these toys were too much for Zelda and Link. Displaying the symbol of the Triforce of Power on his hand, he commanded that they return the Triforce pieces to him. He blasted waves of darkness at Navi, keeping the fairy from getting close to him and discovering his weaknesses. With another evil laugh, the organ and Zelda disappeared, and Ganondorf the Great King of Evil floated in the air.

Ganondorf's first spell knocked the floor down all around him, exposing the room below. Link leaped for the edge before he could fall downward with the floor. Ganondorf shot bolts of energy at Link, but remembering Phantom Ganon from the forest temple, Link struck the bolts back at Ganondorf. Ganondorf remained floating in the center of the room, hitting back each bolt of energy that Link could return with the Master Sword. At last Ganondorf messed up his timing, and one of his own spells hit him back. With Ganondorf momentarily stunned, Link took the opportunity to shoot a Light Arrow at the Evil King. As the light of justice surged painfully all over Ganondorf's body, the Evil King dropped to the floor, panting.

Link jumped across the gap, and getting out the Master Sword, was able to hit the Evil King a few times before he revived and began floating in the air again. Link jumped back to the edge, and the battle raged on. Sometimes Ganondorf paused to gather up all his strength, and cast a more powerful spell. This spell split up, and each piece of the electrical spell chased after Link. Rolling at the last second, it missed Link and hit the floor, creating another gap. Ganondorf cast this spell several times, but by this time Link had discovered how to counteract it. Using the Spin Attack, Link knocked the spell back at Ganondorf, who was hit once again.

When Ganondorf could take no more blows from the Master Sword, he started to succumb to death. Expressing disbelief that he could have been beaten by this kid, he coughed blood and yelled Link's name. With one final roar, he raised his arms and consumed everything in sight with energy. When the stained-glass windows had all melted away, Link and Ganondorf remained standing in the open air, at the very top of Ganon's Tower. Ganondorf remained standing for a moment and then, collapsing to his knees, fell face first on the ground.

The crystal holding Zelda prisoner descended slowly to the ground, and then faded away. Zelda opened her eyes. Looking at Ganondorf crumpled on the ground, she called him a pitiful man who could not control the power of the gods without a righteous mind. Suddenly the castle rumbled and shook, and Zelda realized that with his last breath Ganondorf was trying to crush them in the ruins of his tower. She told Link to follow her out, and started running. They came to a barred entrance, and Zelda used a spell to open it. Zigzagging in and out of the tower, Link and Zelda avoided burning rubble and falling stones, while Zelda opened barred entrances. Time was running out when suddenly Zelda was trapped in a ring of fire, and Link was forced to battle two Stalfos' to free her. They exited Ganon's Castle just in time, and from a safe spot watched the dark Tower crumble and collapse into itself.