Hyrule has been plagued with drought and pestilence. In this time of trouble, the King of Hyrule was approached by a powerful wizard named Agahnim. This wizard used magic never seen before to restore Hyrule.

Then, to everyone's surprise, they found it was Ganon, escaped from the dark world. Secretly, he killed the king of Hyrule, and ruled over the land, though no one outside the castle was aware of this. Agahnim captured Princess Zelda, but before she was captured, the Princess sent out a telepathic message to Link, a descendant of the Hero of Time.

Link's uncle received this message too. Though he knew it was meant for Link, he begged Link to wait until morning, for there was a great storm. Link entered the castle through the sewers, where he found his uncle, who was severely injured. His uncle gave him his sword and shield, and then Link entered the castle.

After fighting his way through Agahnim's minions, Link managed to rescue Princess Zelda from the castle. He was told that to defeat the wizard Agahnim, he must use the Master Sword that the Hero of Time had used to slay Ganondorf Dragmire and seal him away. This was in the Mysterious Forest, but he needed three pendants. After battling long and hard to get these, he pulled the Master Sword out of the pedestal, and fought his way to Agahnim. He used the sword to repel Agahnim's dark magic, but before he defeated the evil wizard, Agahnim sent Link into the Dark World.

There Link received a telepathic message from a wise man called Sahasrahla. Sahasrahla told Link that Agahnim had sent the seven descendants if the sages into the Dark World trapped inside crystal cocoons, including Zelda. He was to free them before Ganon could return to Hyrule to control the land. Link travelled far and wide, and fought many hard battles, but eventually he freed all of the descendants of sages. Then he travelled to Ganon's tower, on top of Death Mountain, where Agahnim revealed himself as Ganon. Link managed to defeat Agahnim, but then the dark lord transformed into a bat and flew to the Pyramid of Power. Link followed after him, and defeated Ganon. Finally, Hyrule was at peace.

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