Ganondorf's rise to power and the hero's quest to defeat him and bring peace to the land of Hyrule once again. The game opens with the hero's mentor and protector, The Great Deku Tree, sending a fairy, Navi, to inform the hero about his new responsibilities. After gathering the necessary equipment, Navi escorts the hero to the Great Deku Tree who explains that Ganondorf has come to the land of and is vying for power. He tells the hero that Ganondorf has cursed him and then proceeds to ask the hero to break the curse. The hero then enters the Great Deku Tree which is also the first dungeon. Inside he fights his way to the dungeon's boss and source of the curse, Queen Ghoma, and defeats her. After the hero's success, the Great Deku Tree reveals that even though his efforts were successful he was doomed from the start. He then tells the tale of Ganondorf and theTriforce and tells the hero he must travel to Hyrule Castle to meet the Princess Zelda, after which he dies.
The hero leaves his home in Kokiri Forest, but is stopped by Saria on the bridge leading out. She gives him the Fairy Ocarina and tells him to remember her. The hero then travels to Hyrule Castle and indeed meets Princess Zelda. She tells him of her dream and about the Spiritual Stones and the . She then asks him to collect the other two spiritual stones. After this meeting the hero is taught the song Zelda's on his ocarina by Impa who leads him out of the castle and shows him the way to Kakariko Village, which lies beneath the Gorons' home in Death Mountain. He meets the leader of the Gorons, Darunia and helps him deal with a problem in Dodongo's Cavern. Afterward, Darunia gives him the Spiritual Stone of Fire or Goron's Ruby in return. The hero then travels to Zora's Domain where he saves Ruto of the Zora's. She then gives him the Spiritual Stone of Water or Zora's Sapphire in return and mentions it to be an engagement ring. The hero then hurries back to Hyrule Castle. At the gate, however, he is stopped by Zelda who is riding away with Impa as if escaping. manages to throw an object to the hero before disappearing into the distance. Ganondorf then comes out of the town and asks about the direction the Princess went. The hero attempts to confront him and Ganondorf defeats him easily then rides off. The hero retrieves the object which is in fact the Ocarina of Time and learns how to play the of Time. He continues, undaunted, to the Temple of Time where he opens the Door of Time and finds the Master Sword.
After removing the Master Sword from the Pedestal of Time, the hero falls into a deep sleep for seven years during which time Ganondorf enters the Sacred Realm, which the hero opened, and takes the Triforce for himself. When he awakens he discovers that much has changed during the seven years he spent sleeping. Rauru, the Sage of Light, explains everything that has happened including the fact that Ganondorf has taken over the world and reveals the hero's destiny: to awaken as the Hero of Time. Then Rauru tells him to add the power of the other Sages to his own and gives him the Light Medallion before returning him to the Hyrule now ruled by Ganondorf. There the hero encounters a mysterious being named Sheik, who claims to be the last of the Sheikah. Sheik tells him that he must travel to and explore the five temples to awaken the five other sages, who will lend him their power to defeat Ganondorf.
The hero travels to each of these temples, not to mention through space and time as well, and awakens its sage, often finding that the sage is a friend or acquaintance. Saria awakens as the Sage of the Forest in the Forest Temple; Darunia awakens as the Sage of Fire in the Fire Temple; Ruto awakens as the Sage of Water in the Water Temple; Impa awakens as the Sage of Shadow in the Shadow Temple; and Nabooru awakens as the Sage of Spirit in the Spirit Temple. He collects their power in the form of a medallion. With these medallions in hand, the hero travels to the Temple of Time once more where he encounters Sheik and discovers that he was actually Zelda all along. She tells him that when Ganondorf tried to take the Triforce it split into three and only the Triforce of Power remained in his hand. The Triforce of Courage went to him, Link, and the Triforce of Wisdom went to her. Ganondorf then captures the , but not before she provides the hero with her own power in the form of the Light Arrows.
The hero travels to Ganon's Castle and enters it with the help of a bridge created by the Sages. He destroys the barriers that protect Ganondorf, each in the form of the element of each Sage, and proceeds into the Tower. He climbs up to room and confronts him for a final showdown, in which he utilizes the power hidden in the Master Sword and the Light Arrows to weaken and then defeat Ganondorf. However Ganondorf, in his dying throes, uses the last of his power to damage the castle causing it to collapse. The hero and Princess Zelda manage to escape, but before they can leave the ruins they are confronted by Ganon, Ganondorf's true form. Ganon disarms the hero, forcing him to resort to Light Arrows and anything at his disposal. He manages to knock Ganon out for a few seconds, buying him enough time to retrieve the Master Sword. The hero defeats him once again, and then, with the aid of the six sages and Zelda who is the seventh and leader of the Sages, traps Ganon in the Sacred Realm.
The Princess thanks the hero, and apologizes for all the hardships she put him through. Then she asks for the Ocarina of Time and being a Sage she is able to return him to his original time. In the ending we see Hyrule has been saved and the people party because of it, although not everyone is too happy. Then we see Link, as a child, go to Zelda once more.