Cia is a sorceress that watches over the equilibrium within the Triforce. She also has the power to see through time, and it is through this power that she comes to discover Link. Though she comes to love him from afar, the realization that she could never be with him distracts her. It is at that moment that an evil presence takes the opportunity to force its way into her body and take hold of her while pushing the good in Cia's heart out. This expelled "good" side manifests as a separate being named Lana.
Under the influence of the evil power, Cia declares war on Hyrule with her subordinates Volga and Wizzro. As her plan unfurls, she opens up portals to three eras of Hyrule's past, in which fragments of a great evil are sealed away. Though Lana and her allies try to stop her, she and her minions manage to work with Zant and Ghirahim to release the fragments from the past. She subsequently succeeds in stealing away the Triforces of Courage and Wisdom from Link and Sheik, claiming the whole Triforce for herself.
With the Triforce in Cia's possession and three of its fragments freed, the evil force inside her feels she is no longer needed. The three fragments leave her body and join together, revealing the evil force as Ganondorf as he is restored to the flesh. But as the fourth fragment of his being is still sealed away, he is not whole. When he attempts to take the Triforce from Cia, she foils his plan by sending the Triforce pieces of Courage and Wisdom back to their proper bearers, and then spirits him away.
Though she manages to rid herself of the evil that had taken hold of her, Cia's being is thoroughly corrupted. She is intent on reclaiming the remaining pieces of the Triforce, as well as Link, for herself. When Link later claims the Master Sword, she sets a trap, using his overconfidence to lure him in and use his weakness to create minions in the shape of Dark Link. When that plan fails, she is backed into a corner, and eventually faces the Hyrulian army in a final battle. Cia uses every ounce of energy in her soul in an effort to bring the Hyrulians to their knees, but in the end, she is defeated.
In her final moments, Cia laments her confusion to Lana, believing her defeat is what she wanted, and doesn't understand how Lana could stand not being able to have Link. But Lana informs her that she understands that people can't always be with the ones they desire, and she accepts that. With her last breath, Cia compliments Lana as their better half, and then dies. As her body vanishes, the Triforce of Power is freed from her, and Lana claims it in her stead.
As a Player Character
Upon the release of Hyrule Warriors, Cia was strictly an NPC. A forthcoming free update to the game will make her a playable character. As a player character, Cia fights with her staff, which can manifest a whip-like extension. The game's first DLC expansion, the Master Quest pack, will come with a five stage side-story starring Cia and explain how she came to meet Volga and Wizzro.