Link is in a coma after his intense final(?) battle with Ganondorf, and while his friends are trying to keep him alive, and possibly wake him up, he's dreaming of what it would be like if the Triforces were given to different people. In addition to this, he's being pestered by someone who has direct contact with the goddesses.

When Hylia first wakes up, she is in an empty world with nothing but a small glowing triangle. As she learns how to use the power that the triangle possesses, she realizes that there is more to the world that she created than she realized. She and the six people she woke up with must avoid the evil being created by the Hexforce to keep the balance, concluding with an epic battle.