While rescuing Zelda from Ganon, Link disappears into the Still World after falling into a mysterious rift; similar rifts appear throughout Hyrule, causing others to disappear into the Still World, including its king and his advisors, General Wright and Minister Lefte. Upon Zelda's return to Hyrule Castle, imposters of the king and his advisors frame her for causing the rifts and imprison her in the castle's dungeons to be executed. Zelda escapes with help from the fairy Tri, who gives her the Tri Rod and accompanies her on her journey throughout Hyrule to repair the rifts and rescue those trapped in the Still World.

During her adventure, she confronts an imposter of Link and rescues the real Link from Ganon after confronting and defeating him in Hyrule Castle, but Ganon is revealed to be an imposter created by the primordial evil Null, who also possesses the ability to create echoes and captures Link. After Zelda repairs the rifts affecting the shrines of the Golden Goddesses, Din, Nayru, and Farore, they explain to her that Null resided in the void that existed before reality, consuming life when it developed in order to remain the only being in existence. The Goddesses created the universe over the void to seal away Null, causing it to resent them. After Hyrule was founded, Null attempted to break its seal by creating rifts in order to destroy it and return existence to the void. To counteract the rifts, the Goddesses sent the Tris to repair the rifts and return to them once their purpose was fulfilled.

Null attempts to take the Prime Energy for itself by creating an echo of Zelda, whom the Goddesses deemed worthy of possessing part of its power along with Link. However, as Null has an unbalanced heart, it only obtained the Triforce of Power, with Wisdom going to Zelda, and Courage creating a rift leading to Link. Zelda's echo enters, to obtain Link's piece, with Zelda in pursuit. Zelda defeats the echo of herself, but Null obtains the Triforce piece regardless and creates massive rifts spanning nearly all of Hyrule. Zelda frees Link, and they ultimately confront and destroy Null. The Tris, powered by a wish from the complete Triforce, repair the rifts and return to the Goddesses while Zelda reunites with the king.