Searching for clues about the other Sages, Link went to Kakariko Village. He found the city engulfed in flames. Spotting Sheik by the town well, Link ran over to him. Sheik told Link to stay back, and suddenly the top of the well blew out, landing behind Link. Something invisible grabbed Sheik, picking him up and throwing him high in the air.

Link rushed over to Sheik to see if he was hurt badly, but sensed that something evil was afoot. He was chilled to the bone to see a shadowy shape crawl quickly all over the buildings of Kakariko, and readied the Master Sword. The shadow rushed over the ground at Link, and Link readied himself for a Spin Attack. But the Hero of Time was no match. He struggled and fought, but he was overcome by the darkness...

When Link came to, Sheik was attending to the unconscious hero. He told Link,

A terrible thing has happened! The evil shadow spirit has been released! Impa, the leader of Kakariko Village, had sealed the evil shadow spirit in the bottom of the well. But the force of the evil spirit got so strong, the seal of the well broke, and it escaped into the world!! I believe Impa has gone to the Shadow Temple to seal it up again, but... she will be in danger without any help! Link! Impa is one of the six Sages. Destroy the evil shadow spirit and save Impa!

Sheik told Link that the entrance to the Shadow Temple lay beneath the graveyard, and taught him the Nocturne of Shadow, which would lead him to the Shadow Temple. Promising to look after the village, Sheik disappeared.

Link played the Nocturne of Shadow, warping to the Shadow Temple. When he entered, a wicked-sounding voice whispered in his ear:

The Shadow will yield only to one with the eye of truth, handed down in Kakariko Village.

Link talked to the inhabitants of Kakariko, and an old man told him that a long time ago there lived a man who had an eye they said could see the truth. His house had been where the well currently was. Link went to the bottom of the well, but saw that the entrance to the well had been blocked off. Link talked to a strange organ grinder in the windmill, who taught him a strange song, the Song of Storms. A child with an ocarina had messed up the windmill seven years ago by playing this song. Link realized that he was the child, and though he had never done such a thing, he was sure the musician was talking about him.

His curiosity piqued, Link wondered whether it was possible to travel back to the past. He traveled back to the Temple of Time, braving the zombie-infested Hyrule Castle Town Market, and found Sheik in front of the Pedestal of Time. He told Link to drive the Master Sword back into the Pedestal of Time if he wanted travel back in time seven years. Before Sheik disappeared, he taught Link the Prelude of Light, which would take Link to the Temple of Time quickly.

Link did as Sheik had told him, and was surrounded by blue light. When he opened his eyes, he was young again, and Hyrule was beautiful again. Link went through the now busy Hyrule Castle Town Market, and walked to Kakariko Village. The well was full of water, so Link went into the windmill and played the Song of Storms. The windmill spun out of control, making the organ grinder dizzy. This drained the well, and Link worked his way down to the bottom of the well and braved the dangers inside. The evil place was full of restless spirits telling him to get the "eye of truth." Link dodged traps, and eventually fought with the strange enemy Dead Hand. In the next room Link obtained the Lens of Truth, with which he could now see all the invisible traps that evil spirits could place before him.

Link played the Prelude of Light to warp back to the Temple of Time, and pulled the Master Sword out of the Pedestal of Time. When he woke up, he was back in the dismal world of the future ruled by Ganondorf. Playing the Nocturne of Shadow, Link was transported to the Shadow Temple. Link used the Lens of Truth to uncover hidden pathways, and found out that he needed to have "sacred feet" in order to cross the "valley of the dead," a large pit. Link fought another Dead Hand to obtain the Hover Boots, which decreased his friction with the ground but allowed him to float in the air momentarily.

Link hovered across the valley of the dead, and, with the Lens of Truth, navigated evil traps and fought vile warriors. Link found a mysterious ferry boat, but it was a trap. Stalfos' dropped out of nowhere, and Link had to leap to safety before the ship sank into the foggy void. In the bowels of the Shadow Temple, Link faced Bongo Bongo, the evil shadow spirit. Bongo Bongo made his body invisible, and his hands beat on the platform Link was standing on, making Link's footing unsure.

Link put on the Hover Boots, and now no matter of shaking could unsettle Link's balance. He pulled out the Fairy Bow and shot arrows at Bongo Bongo's hands. The shadow monster charged at him, and Link looked through the Lens of Truth to pinpoint the monster's huge red eye. Aiming carefully, Link shot an arrow into the vulnerable red sphere, stunning the evil spirit. Bongo Bongo tasted Link's sword, and was defeated after a long battle.

Link was transported to the Chamber of Sages, where he witnessed Impa's awakening as the Sage of Shadow.

The boy with the noble Zelda's Ocarina... As I expected, you have come. I am Impa, one of the Sheikah. I am Princess Zelda's caretaker, and I am also the Sage who guards the Shadow Temple. We Sheikah have served the royalty of Hyrule from generation to generation as attendants. However... On that day seven years ago, Ganondorf suddenly attacked, and Hyrule Castle surrendered after a short time. Ganondorf's target was one of the keys to the Sacred Realm, the hidden treasure of the Royal Family - The Ocarina of Time! My duty bound me to take Zelda out of Ganondorf's reach. When last I saw you, as we made our escape from the castle, you were just a lad. Now I see that you have become a fine hero.

Impa told Link that Zelda was safe, and that soon she would meet him face-to-face and explain everything. At that time the Sages would seal Ganondorf and return peace to Hyrule. She requested that Link protect Zelda on her behalf. Giving him the Spirit Medallion, which contained her power, Link was warped back to the graveyard in Kakariko Village.