- "I never imagined a boy like you could give me so much trouble. It's unbelievable that you defeated my alter-ego, Agahnim the Dark Wizard, twice! But I will never give you the Triforce. I will destroy you and make my wish to conquer both Light and Dark Worlds come true without delay."
- — Ganon
Ganon was once an ordinary thief named Ganondorf who stumbled across the Triforce in the Golden Land. Upon touching the Triforce, the Golden Land was altered to his image, becoming the Dark World. Ganon himself was altered into a powerful being capable of incredible feats of might and magic.
Not satisfied with his own world, Ganon sought to conquer Hyrule, as well. However, he was stopped by the actions of the Seven Wise Men and was sealed away. From inside the Dark World, however, Ganon was able to construct an avatar named Agahnim. Upon reaching Hyrule, Agahnim began to use magic in order to seal away the descendents of the Seven Sages in order to free Ganon. Once Princess Zelda, the final descendent, was sealed away, the Dark World was unleashed and Ganon was freed.
After freeing the Seven Maidens, Link ascends Ganon's Tower and defeats Aghanim, who Ganon describes as his alter ego. Ganon then rises from Agahnim's body before transforming into a bat and flying to the Pyramid in the center of the Dark World, where he breaks a hole through the Pyramid's top. Link uses the flute to call his bird and follows Ganon to the Pyramid. Inside, Link and Ganon battle for the future of Hyrule.
Link defeats Ganon with the help of the Silver Arrows and a doorway opens. Link enters it and finds himself in a hall where the omniscient Triforce lies. Wishing with all of his heart for Ganon's evil deeds to be undone, Link touches the Triforce, and his wishes are granted. The Dark World disappears and the land of Hyrule is restored to peace.
Ganon warps across the room, throwing his trident like a boomerang. After Link deals a certain amount of damage with his sword, Ganon will generate rings of fireballs around himself, which will turn into bat shapes similar to Fire Keese and fly at Link. After Ganon has taken more damage, he will cause the bordering floor to collapse and send Fire Keese in a spiral pattern, which leave a trail of flame. Ganon then makes the room go dark, rendering himself invisible, and warps around the arena shooting more Fire Keese straight at Link. Link must relight the torches with the Lantern or the Fire Rod, making Ganon visible again so that he can stun him with a sword slash. Link must then shoot Ganon with a silver arrow. After Link repeats this four times, Ganon is defeated.
If Link falls off the edge of the battlefield after Ganon makes the floor collapse, the battle ends, and Link finds himself in a corridor with a Telepathic Tile through which Sahasrahla will advise him. The battle against Ganon must then be fought again from the beginning. This happens even after Ganon is defeated.