Zelda was relieved that it was finally over, and Navi apologized for not helping in the battle before. Suddenly, from within the rubble, they all heard a noise. Link went to investigate, and a ring of fire surrounded the ruins, separating Link and Navi from Zelda. Out of the rubble burst Ganondorf, who with glowing eyes and labored breathing, triumphantly displayed the symbol of the Triforce of Power on his hand. Roaring, Ganondorf was consumed by blue energy, and before Link's astonished eyes transformed into a huge monster. What dropped to the ground was Ganon, Ganondorf's most powerful form, transformed by Ganondorf's blackest desires. Ganon towered above Link, drawing out two swords bigger than Link himself. Link bravely drew out the Master Sword, but before he was ready Ganon knocked it out of his hand. The Blade of Evil's Bane flew through the air and through the ring of fire, striking into the ground right next to Zelda. Navi vowed that this time she would fight together with Link, and the final battle began.

If Ganon had a weakness, Navi couldn't find it. Link was on his own, and had to innovate. He couldn't approach Ganon from the front, or Ganon would slash at him with his huge swords. Ganon chased Link slowly all around the dark ruins, while Link tried different strategies. Link discovered that he could stun Ganon momentarily with a Light Arrow, and also found that he could roll between Ganon's legs and come out behind him. Link noticed for the first time that Ganon had a tail, and getting out the Megaton Hammer, he swung with all his might. Ganon roared with pain, and spun around to face Link again. Link kept on striking Ganon's tail until the evil monstrosity fell to the ground, stunned.

While Ganon recovered, the ring of fire subsided, and Zelda yelled at Link to come get the Master Sword. Link plucked it out of the ground and rushed back into battle. Ganon was desperate now, and fought harder than before. However, Link now had the Blade of Evil's Bane, and Ganon's tail felt the wrath of its purifying blows. Ganon was stunned again, and suddenly a beam of light shot through him. Zelda was using her power to hold the Evil King, and she told Link to use the Master Sword to deliver the final blow. The Master Sword glowed blue with power, and Link slashed at Ganon's head four times. With a pained roar, Ganon sprung up, thrashing around with his arms.

Zelda, the leader of the Sages, told the six other Sages telepathically that the time had come to seal the Evil King. Rauru and the five other sages in the Chamber of Sages prayed to the ancient creators of Hyrule, telling them to open the sealed door and send the Evil Incarnation of Darkness into the Sacred Realm. A wave of energy flowed from the Chamber of Sages, and Ganon, back in the form of Ganondorf, was sent to his Evil Realm and locked inside. Before he faded out of sight, Ganondorf cursed Zelda, Link, and the Sages. He vowed that when this door was opened he would exterminate their descendants. As Ganondorf disappeared, he boasted that he still held the Triforce of Power in his hand.

Zelda and Link floated in a limpid blue sky, surrounded by beautiful white clouds. Zelda thanked Link, and told him:

Thanks to you, Ganondorf has been sealed inside the Evil Realm! Thus, peace will once again reign in this world... for a time. All the tragedy that has befallen Hyrule was my doing... I was so young... I could not comprehend the consequences of trying to control the Sacred Realm. I dragged you into it, too. Now it is time for me to make up for my mistakes... You must lay the Master Sword to rest and close the Door of Time... However, by doing this, the road between times will be closed. Link, give the Ocarina to me... As a Sage, I can return you to your original time with it.

Link gave the Ocarina of Time to Zelda, but her heart was broken. When peace returned to Hyrule, it would be time for them to say good-bye. Taking courage, she told Link to go home, where he was supposed to be, the way he was supposed to be, and regain lost time. As she played the Song of Time, Link was encased in a blue crystal, and floated out of sight. Zelda thanked Link one last time, and told him good-bye.

Meanwhile, all of Hyrule was quiet. Plants were regrowing, and Zora's Domain had melted. No one was at home, because the people of Hyrule were celebrating at Lon Lon Ranch. Everyone, from Mido of the Kokiri, to the displaced Zoras, to Biggoron of the Gorons, was celebrating the demise of Ganondorf. Even the lazy ranch owner Talon and the grumpy worker Ingo were having a jolly time getting drunk together. Saria's Song was played, while Talon's daughter Malon sung along, and everyone danced around a ring of multicolored fires. Even the Sages attended the party, in spirit.

The only one absent was Link, the Hero of Time. After saying good-bye to Zelda, Link traveled back in time seven years. When he opened his eyes he was once again a child, and was standing in front of the Master Sword in the Temple of Time. Sunlight poured in through the windows, and Link slowly walked out of the Temple, leaving the Master Sword behind and the road between times closed forever.

Determined to see Zelda again, Link snuck back into Hyrule Castle and found her at the same window as before. Zelda entrusted the Ocarina of Time to Link. For his noble deeds Link was deemed a hero, and took his place in legends passed down by the Royal Family.