As Link enters the castle's surrounding area and comes in close range of the tower itself, he's shocked to see the changes from the King of Hyrule's time and now. Once bright and marbelesque, the castle is now dark and decrepit.

Nearing the castle, Link sees that there is a deep moat encircling it, seemingly impassable. Combining their power, the Sages create a rainbow platform, bridging the gap and allowing Link to cross over and into Ganon's Tower.

Rauru, Sage of Light, explains to Link that he must destroy seven barriers to enter the main section of the castle. Without delay, Link does just that, eventually arriving at the Forest Barrier.

After a bit of problem solving and bad-guy slaying, Link enters the barrier's central chamber. Destroying it with one shot of a light-imbued arrow, Saria appears, encouraging Link and quickly sending him back to the main hall.

After all of the barriers are dispelled, Link heads upstairs and arrives at Ganon's quarters. Their the two dual, Link eventually getting the upper hand and defeating Ganondorf. Zelda, now free of her crystal cage, realizes that in his last breath Ganondorf is trying to destroy the castle with them in it. Desperately, Zelda and Link run through the crumbling tower and escape, just before it caves in on itself.

Thinking it's over, Zelda and Link are about to rejoice. Suddenly, a loud thump is heard in the direction of the ruins. Link heads toward the sound and Ganondorf, still holding the Triforce of Power, bursts out of the rubble. Horrifically, he morphs into Ganon, his true form, and attacks. However, his might is no match for the Hero of Time, and Link's final blow knocks the great beast to his knees.

Zelda, knowing the time has come to seal away Ganon, calls the six Sages to her. Saria and the others, with Rauru directing them, metamorphose into their incandescent forms and meld together, creating a vortex of light that sucks the Evil King into the Evil Realm. Cursing the Sages and Link, Ganon is nonetheless barred.

Zelda, apologizing for her part in accidentally causing all of the past events to happen, decides to send Link back to the past so he can grow up as he was supposed to. Passing her the Ocarina of Time, she plays her Lullaby, transporting Link permanently back to the past.

Elsewhere in future Hyrule, the races have come together to celebrate the destruction of the evil forces and the banishment of Ganon. Even the Kokiri, usually hesitant to be around strangers, are partying alongside the other Hylian races.

Mido, however, sits off to the side with King Zora, both looking quite depressed despite what good has happened. Saria, Link and Ruto have not yet returned; Mido regrets the way he treated Link, and dearly misses Saria; the King of the Zora's also misses his beloved daughter.

Suddenly, sparks of green and blue light fall from the sky; looking up, both Mido and King Zora see two large, emerald and sapphire balls of light speeding over them, followed by three others. The lights travel to the top of Death Mountain, where there they expand and contort into the five Sages: Nabooru, Ruto, Impa, Darunia and Saria. As the sun rises, bringing the first day of peace, Impa looks up...

In the Temple of Time, Link returns as a boy. Navi, having completed her duty, departs. Link, with one final, decisive look at the Master Sword, steps down from the pedestal and heads out of the Temple.