Once upon a time, wizards tried to conquer the Sacred Realm of Hyrule. The Spirits of Light sealed the wizards' power within the Shadow Crystal and banished them to the Twilight Realm beyond the Mirror of Twilight. Now, an evil menace is trying to find Midna, Princess of the Twilight Realm, and the fragments of the Shadow Crystal to gain the power to rule over both the Twilight Realm and the World of Light.

Midna tells Link about the time before she came to the world of Light and how the evil wizard Zant turned her into her current form. Bitter and angry, Midna only used other people to get her revenge. Link needs Midna's help now more than ever, and his forgiveness may give her the strength to continue the fight. Ahead of them, in the Twilight Realm itself, lie greater dangers than they have faced before, as well as Midna's nemesis, the scheming sorcerer Zant.