Link, the apprentice of a blacksmith, goes to deliver a sword to a captain at Hyrule Castle, only to encounter a mysterious figure named Yuga, who transforms a descendant of one of the Seven Sages, Seres, into a painting. Link underestimates Yuga and is defeated. A merchant, Ravio, proposes help to Link and gives him a bracelet and his items. To Ravio's advice, Link reports the events to Princess Zelda. She gives him the Pendant of Courage; in Hyrule exists three Pendants that once found gives the power to wield the Master Sword. During his search, Link defeats Yuga but is transformed into a painting, letting the latter flee. Yuga's curse is contained into Ravio's bracelet, giving Link the ability to merge at his will.

Link uses his new power to find the other Pendants; successful, Link wields the Master Sword and visits Zelda, only to witness Yuga capturing her into a painting and confronts him once more. Yuga flees into a dimensional crack leading to Lorule. The captured sages are used to resurrect Ganon, which Yuga merges with. Lorule's princess Hilda assists Link by trapping Yuga.

To Hilda's orders, Link treks through Lorule to rescue the Seven Sages across the kingdom's dungeon. Each rescued Sage is kept into the Chamber of Sages. With the Seven Sages rescued, their combined powers create the Triforce of Courage for Link, worthy of wielding it. Link returns to Lorule Castle, confronting Yuga. However, before doing so, Hilda steals Zelda's Triforce of Wisdom. Hilda reveals her goal: long ago, Lorule was once a peaceful kingdom until her ancestors destroyed its Triforce to end a civil war, allowing Lorule to fall into its current ruined state.

Deciding to use Hyrule's Triforce, she sent Yuga to steal the Triforce of Courage from Link, to no avail; she tricked Link into finding it himself for her. With the complete Triforce, Yuga betrays Hilda to get the Triforce for himself. Link confronts Yuga and finally defeats him. He restores the two princesses. During Hilda's apology, Ravio suddenly appears, revealing himself as Link's counterpart. He and Hilda makes amends and decide to help each other rebuilding Lorule.

Link and Zelda return to Hyrule, and use its Triforce to grant their wish; Lorule's Triforce is restored and the kingdom returns to its former glory. Link disposes of the Master Sword in its pedestal and leaves with both the returned Sages and Zelda.