Cid Raines comes into the story after Snow is captured by his special Sanctum unit, led by Fang, whom Snow notices is also a l'Cie. He's brought aboard the lead ship of the brigade, the Lindblum and Cid Raines explains that the Sanctum intends to hold public executions of him and his fellow l'Cie. He manages to convince Snow to help him capture the others in order to save Cocoon, truly believing this to be his Focus. Though, he doesn't intend to deliver them to their deaths, but to help him overthrow the government he finds corrupt and unruly, giving control to the people.
After the party manages to escape from the Palamecia, with the help of the Fal'Cie, Barthandelus, they find themselves in the Fifth Ark, a l'Cie proving grounds. Cid awaits them, revealing he is also a l'Cie whose Focus was to lead them in the right direction to fulfilling their Focus. Ironically enough it turns out their focus is to destroy Cocoon, leading Cid to fight them in order to save Cocoon. After his defeat, the party is still skeptical of Barthandelus' actions, believing all of this to be part of his plans. The victory proves to be bittersweet, for not only did he prove to be a strong ally, he encouraged them to do what they felt was right before fulfilling his Focus and turning to crystal.
Later on, the party is searching for answers to their destiny, and Barthandelus, in his human guise of Primarch Galenth Dysley, is more than happy to reaffirm what he has already told them. He had revitalized Cid and had inserted him as the new Primarch of Cocoon, a puppet bound to incite chaos upon his allies realizing his betrayal to the cause. The party realizes this is their best chance of slipping into the capital city of Eden as uninhibited as possible, so they take Barthandelus' ship back. Cid Raines bears witness to the mayhem unfold, Pulse creatures pouring in through portals implanted by Barthandelus, calmly awaiting his fate. Rygdaea, his direct subordinate infiltrates the palace with his troops, and upon his request, reluctantly executes his Commander.
Before he is shot, he states that "My dream has become nothing but a Fal'Cies fancy."