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Cia was tasked with maintaining the balance of the Triforce, as she was a good person at heart. However, she began to gain strong feelings for a brave young knight named Link, causing her to become jealous of his relationship with Zelda. This allowed her to be corrupted by a mysterious evil entity, who had been thought to be sealed away long ago (by a past Link). Her light side was driven out (which became Lana), turning Cia pure evil. Cia allies herself with the fire-manipulating warrior Volga, and gains the allegiance of Wizzro by giving it a physical body. With her new power and allies she declares war on Hyrule.
Cia sent Volga and Wizzro to attack Hyrule, but Link, Zelda, Impa, and Lana fought against them. Cia opened the Portals of Souls in the eras similar to Ocarina of Time, Twilight Princess, and Skyward Sword. Although Link, Zelda, Impa, and Lana were able to close them with help from Darunia, Ruto, Midna, Agitha, and Fi, the evil entity was able to revive himself through three of his spirit fragments, revealed to be Ganondorf.
Now working separately from Ganondorf, Cia had Wizzro control ghost forces to destroy the heroes, but they defeated him and Link got the Master Sword and used it to kill Wizzro, who in his final words told them that Cia was at the Temple of Souls. There, Link got cocky due to possessing the Master Sword which nearly led to his downfall, as Cia created many Dark Links. The Dark Links were destroyed, and then Ganondorf arrived, who was quickly defeated by Link.
Link and the others took a final stand against Cia at the Valley of Seers. When they gained the upper hand, Cia began transferring her power to her minions to defeat them, not caring what damage it could do to her. After defeating Volga, Link and his team fought Cia, who split into four but was defeated. As she lay dying in Lana's arms, she said neither she nor Lana will get Link's affection, to which Lana says she accepts this. Cia says Lana was always her better half, and fades into nothingness, with Lana obtaining her Triforce of Power.
After Cia's death, the role of antagonist shifts to Ganondorf, who is revived through his fourth spirit fragment.