Six years after the defeat of Ganon and the rescue of Princess Zelda in the events of The Legend of Zelda, Link, now at the age of sixteen, is disturbed by the appearance of a mark on the back of his left hand. Upon seeing this mark, Impa, the nurse of Zelda, tells him the story of how, ages ago, the King of Hyrule had hidden a third part of the Triforce, the Triforce of Courage, in the Great Palace to safeguard it from evil.

Upon the death of the King, his son had searched for the missing Triforce, but its location had been imparted only to the king's daughter, Princess Zelda. Angered upon learning this, the Prince tried to use the power of a Magician to force the truth from his sister. After she refused, the wizard cast a powerful spell upon her to put her into a deep sleep, which caused the wizard to die soon after. Only by uniting the Triforce of Courage with its counterparts, the Triforce of Power, the piece formerly stolen by Ganon, and Triforce of Wisdom - itself Princess Zelda's piece, would Link be able to awake the sleeping princess. Upon hearing this tale, Link receives from Impa six crystals that serve as keys to open the seal on the Great Palace.

As Link learns all of this, the minions of Ganon begin to attack once again. Believing that they could revive their master by pouring the blood of Link over his ashes, they begin to spread across the land, seeking for him in order to kill the hero. Eventually, Link is able to gain the Triforce of Courage by defeating his own shadow. Uniting the three Triforce parts to become complete, Link returns to the Northern Palace to wake the slumbering Zelda at last and save Hyrule once again.