The Central Intelligence Agency (CIA) is one of the principal intelligence-gathering agencies of the United States government. Its headquarters is in Langley, Virginia. Its employees operate from U.S. embassies and many other locations around the world.
In Las Vegas, Nevada in 1962, CIA agents Moira MacTaggert and Levene monitor the activities of the Hellfire Club. MacTaggart follows U.S. Army Colonel Hendry, where she sees Sebastian Shaw, Emma Frost, Riptide and Azazel, witnessing the mutant powers of the three latter. After Shaw threatens Hendry, Azazel disappears with the officer; moments later he is in the War Room, Hendry advocates that U.S. install nuclear missiles in Turkey.
MacTaggert seeks Charles Xavier's advice on mutation, and takes Xavier and his foster sister Raven to convince the CIA's Director of Intelligence John McCone that Shaw was a threat. After convincing them that mutants exist they are taken to a covert facility, but where a sting operation against the Hellfire Club is organized. During the attack, Erik Lehnsherr, uninvolved in the operation, attacks Shaw, and when the Hellfire Club esacpes in their submarine, Lehnsherr tries to stop them, but Xavier prevents him so that he does not drown.
Lehnsherr joins Xavier and Raven at the CIA facility, where they meet Hank McCoy, another mutant that Xavier accidentally outs. McCoy and Xavier use a prototype Cerebro to locate and recruit mutants to train to stop the Hellfire Club. During process, both Xavier and Lehnsherr are able to recruit Angel, Darwin, Havok, and Banshee. Logan was also considered, but he rudely dismisses Xavier and Lehnsherr.
Later on, Xavier, Lehnsherr, MacTaggert and Levene become part of a CIA covert ops-mission into Russia to apprehend Shaw - which required breaking into the military retreat of a high-ranking Soviet general. However, Emma Frost came in Shaw's place, and Xavier and Lehnsherr are able to capture her and discover the Hellfire Club's plans. Frost is later imprisoned at the CIA Headquarters.
During the climax of the Cuban Missile Crisis, senior CIA official William Stryker Sr., already antipathetic towards mutant-kind, organizes a joint U.S.-Soviet strike against the mutants. This effort backfires, and nearly results in the destruction of the U.S. and Soviet fleets.
A month after the Crisis, the newly formed Brotherhood of Mutants breaks into the CIA's headquarters and frees Emma Frost.