The king of Hyrule had recently appointed a new chief advisor. He was a mysterious wizard by the name of Agahnim. When the king fell ill, Agahnim came into control. It wasn't very long before some of the guards in the castle began to act strangely, and many other soldiers feared what might happen to themselves. Many also noticed strange late-night experiments taking place in the top tower of the castle. One by one, Agahnim was causing seven young girls to disappear. They were all decendants of the seven sages who banished Ganon into the Sacred Realm.

Two decendants of The Hero, another boy named Link and his uncle, lived in a house not far from the castle. Late one night, while Link was in bed, both of them heard a telepathic message from Princess Zelda. She was calling for help, explaining that she was the last of the girls that Agahnim would do away with. Not knowing that Link also heard the message, his uncle told him that he was leaving for the night and that Link should stay in the house. Carrying the family sword and shield, he left. Link however, just had to see what was going on. After grabbing a lamp, Link set out into the dark and stormy night...

After entering the castle through a secret entrance, Link found his uncle, wounded and unable to move on. He gave Link the sword and shield, and told him that he must rescue Zelda. Link traveled through the castle and fought off the guards who had been warped by Agahnim's influence. In the deepest part of the castle dungeon, Link found Princess Zelda. He took her through the castle sewers, which connected to a secret passage in the sanctuary west of the castle. Zelda would be safe in the sanctuary with the priest.

If Agahnim had done away with Zelda, the last remaining decedant of the sages, then the seal to the Sacred Realm would have been broken...

Link discovered that the only way he could defeat Agahnim was with the Master Sword, which could be drawn only with the three pendants of Power, Wisdom, and Courage. The pendants were found in three dungeons across Hyrule. It could be assumed that some time between when Ganon was banished into the Sacred Realm, and the present time, the essences of the Spiritual Stones were sealed in the pendants, and placed in the dungeons. The Master Sword had also been moved from the Temple of Time into the Lost Woods.

Link traveled all through Hyrule and obtained the three pendants. He drew the Master Sword, but before he could even leave the Lost Woods, he received a telepathic message from Zelda: she had been captured by Agahnim's soldiers!

Link immediantly went to the top of Hyrule Castle, where he saw Agahnim cause Zelda to disappear before his eyes. Link then fought Agahnim with the Master Sword, but still could not defeat him, because Agahnim cast Link into the Sacred Realm before he could do so.

In the Sacred Realm, Link found himself on top of the Temple of Light. The Sacred Realm however, had become the Dark World. Apparently, the Sacred Realm takes the form of the heart of the one who owns the Triforce. Since Ganon still owned the Triforce, the Sacred Realm was in the form of a warped Hyrule. Many places seemed to correspond with those that Link was familiar with, but they were very dead and gloomy. The Dark World is where Agahnim had placed the decendants of the sages. They were held within seven dungeons throughout the Dark World. Link needed their power to break the seal of Ganon's Tower.

Once Ganon's Tower was opened, he scaled it to the top, where he once again fought Agahnim. Agahnim turned out to be Ganon's alter-ego, who unlike Ganon, was able to enter Hyrule. The reason Ganon wanted to break the seal was that he was not content with ruling only the Dark World. He planned to invade Hyrule with the troops he had amassed in the Dark World so that he could rule both worlds.

Ganon fled to the Temple of Light, and Link fought him there. Link killed him, and at long last, Ganon was no more. As the one who killed him, Link was entitled to the entire Triforce. How Ganon was able to have the entire Triforce is unclear. Perhaps after the Link and Zelda who imprisoned him died, the Triforces of Wisdom and Courage came to the one who owned the Triforce of Power.