In October 1962, U-2 surveillance photos reveal that the Soviet Union is in the process of placing missiles carrying

nuclear weapons in Cuba. President John F. Kennedy (Bruce Greenwood) and his advisers must come up with a plan of action to prevent their activation. Kennedy is determined to show that the United States will not allow a missile threat. The Joint Chiefs of Staff advise immediate U.S. military strikes against the missile sites followed by an invasion of Cuba. However, Kennedy is reluctant to attack and invade because it would very likely cause the Soviets to invade Berlin. Citing The Guns of August, Kennedy sees an analogy to the events that started World War I, where the tactics of both sides commanders had not evolved since the previous war and were obsolete, only this time nuclear weapons are involved. War appears to be almost inevitable. The Kennedy administration tries to find a solution that will remove the missiles but avoid an act of war. They settle on a step less than a blockade, which is formally regarded as an act of war. They settle on what they publicly describe as a quarantine. They announce that the U.S. Naval forces will stop all ships entering Cuban waters and inspect them to verify they are not carrying weapons destined for Cuba. The Soviet Union sends mixed messages in response. John A. Scali, a reporter with ABC News, is contacted by Soviet "emissary" Aleksandr Fomin (Boris Lee Krutonog), and through this back-channel communication method the Soviets offer to remove the missiles in exchange for public assurances from the U.S. that it will never invade Cuba. A long message in the same tone as the informal communication from Fomin, apparently written personally by Soviet Premier Nikita Khrushchev, is received. This is followed by a second, more hard line cable in which the Soviets offer a deal involving U.S removal of its Jupiter missiles from Turkey. The Kennedy administration interprets the second as a response from the Politburo, and in a risky act, decides to ignore it and respond to the first message, assumed to be from Khrushchev. There are several missteps during the crisis: the defense readiness level of Strategic Air Command (SAC) is raised to DEFCON 2 (one step shy of maximum readiness for imminent war), without informing the President; a nuclear weapon test proceeds (Bluegill Triple Prime) and a routine test launch of a U.S. offensive missile is also carried out without the President's knowledge. After much deliberation with the Executive Committee of the National Security Council, Kennedy secretly agrees to remove all Jupiter missiles from southern Italy and in Turkey, the latter on the border of the Soviet Union, in exchange for Khrushchev removing all missiles in Cuba. Off the shores of Cuba, the Soviet ships turn back from the quarantine lines.

Secretary of State Dean Rusk (Henry Strozier) says, "We're eyeball to eyeball and I think the other fellow just blinked." The film ends as O'Donnell and his family are getting ready to go to church but is called to the White House just moments before leaving for church.