The land of Hyrule in a state of fear because of strange happenings that have occurred recently. On a stormy night, Princess Zelda and the shrine maidens fear that the reason for these events is that Vaati's seal is weakening. She summons Link and brings him to the castle so he can protect her and the other maidens while they open the portal to the Four Sword Sanctuary. When they do, however, Shadow Link appears, who kidnaps the maidens of the Shrines and seals them inside their crystals. Link pulls the Four Sword out of its Pedestal, splitting into three clones of himself to destroy his doppelg nger. However, the seal that imprisoned Vaati breaks and releases him from his prison once again, wreaking havoc on the once peaceful kingdom of Hyrule.

As Link and his clones wander the overworld of Hyrule Field on their quest to restore peace to Hyrule, they learn that the creation of Link's evil counterpart and the release of Vaati is only a small part in a larger plot to conquer the kingdom of Hyrule. Things complicate as the dimension of the Dark World appears and people are being abducted throughout Hyrule. The four Links learn that the knights of Hyrule have mysteriously disappeared and evil versions of them have been creating havoc, allowing Hyrule castle to be taken over and monsters to appear throughout the land. The four Links agree that they will defeat Vaati, and rescue Zelda to restore peace to Hyrule.

It is revealed that the true villain is Ganon, who obtained his powers after stealing a powerful trident containing dark energy that was previously hidden away within a pyramid, and used it to seize control over substantial portions of Hyrule. In order to further his plans and distract Link from interfering in his bid for further power, Ganon stole the dark mirror and used it to create Shadow Link, who was eventually sent to kidnap the shrine maidens and trick Link into releasing Vaati. Furthermore, he uses the Dark Mirror to abduct people and turn them into his minions.

The four Links save the shrine maidens, retrieve the Dark Mirror and stop Shadow Link from respawning once and for all. The four heroes head forth to the Palace of Winds and defeat Vaati, leading them into their final battle with Ganon. Trying to stop him from plunging the world into chaos, the four Links use the Power of the Shrine Maidens, including Zelda, to defeat Ganon, striking through him. After defeating Ganon, the four Links firmly seal him inside the Four Sword. Peace returns to Hyrule and the people celebrate as all traces of evil that plagued Hyrule are vanquished. With Ganon defeated and sealed inside, Link returns the Four Sword back to its resting pedestal and the four Links become one again, while the Maidens of the Shrine use their powers and create a barrier around the Four Sword.