The United States continued to strategize for the ouster of Fidel Castro, in the aftermath of the " Bay of Pigs" debacle. At the same time, the Soviet Union stepped up aid to Cuba. In August 1962, reports reached Washington of a significant increase in Cuban aid. Over the previous month, twenty Soviet ships arrived in Cuba carrying military supplies.

This military buildup was unprecedented. Khrushchev had decided to try and change the strategic balance with the US, by installing medium-range missiles in Cuba. Khrushchev hoped his actions would deter the US from attacking Cuba, while strengthening Cuba's ties to the Soviet Union and giving the Soviets additional leverage in Berlin.

Khrushchev thought he could accomplish all this without provoking a confrontation with the US. The Kennedy administration was worried about the Soviet military buildup, although it was initially unaware of its exact nature. Reconnaissance photos soon made it clear that the Soviets were installing Surface-to-Air (SAM) -2 anti-aircraft missiles in Cuba. The SAM-2 missiles were useful only against very high flying aircraft, such as U-2 planes. The US was in a quandary. If the missiles were not being installed to protect against an invasion, they were obviously there to protect something else.

Theories abounded throughout September and early October, but there was no hard evidence. As a result, President Kennedy authorized a U-2 flight over Cuba. Bad weather over Cuba delayed the flight for a few days. On October 14th, the sky over Cuba cleared and the U-2 flight took place. By the following night, photo experts had come to the indisputable conclusion that the Soviets were building medium-range missile sites in Cuba.

At 8:45 am on Tuesday morning, October 16, US National Security Advisor, McGeorge Bundy knocked on the President's door and broke the news to him. Kennedy immediately asked that a meeting be set up with key advisors. The advisors were: Lyndon Johnson, Dean Rusk, Robert McNamara, Robert Kennedy, General Taylor, John McCone, Douglas Dillon, Adlai Stevenson, McGeorge Bundy, Ted Sorenson, George Ball, Roswell Gilpatric, Llewellyn Thompson, Alexis Johnson and Edwin Martin. This group became known as the " Excom" ( the executive committee) In addition, Dean Acheson and Robert Lovett attended some of the meetings.

Initial discussions centered on the nature of a possible military response. Those response options ranged from a swift, sudden bombing of Cuba, to a declaration of war and an invasion. Slowly, a consensus developed for an alternative tack: €˜a blockade against Cuba€™. There were a number of reasons for the shift. First, a surprise attack on the missile sites reminded many of Pearl Harbor in reverse. Second, it soon became clear that there was no such thing as a " surgical air strike" to remove the missiles. It would take almost 1,000 sorties to accomplish destruction of 90% of the mission. In addition, the administration was convinced that the Soviets would respond in Berlin where the US was much more vulnerable. And, it was felt that foreign governments would not understand the need for such drastic actions. Thus, the decision was made to blockade, which was given the name " quarantine" . For almost a week, meetings took place to decide on a course of action. On Thursday, Soviet Foreign Minister Andrei Gromyko had a meeting with the President. Gromyko gave his assurances that the Soviets would never place any offensive weapons in Cuba.

On Monday, October 22, 1962 Congressional leaders were brought to the White House and informed of the latest developments. The meeting was difficult, with Kennedy later describing it as one of his toughest. However, Congressional leaders from both parties agreed to rally around the President. After the meeting, Kennedy joked with Hubert Humphrey that if he€™d known the job was this tough, he would not have beaten Humphrey in West Virginia. Humphrey responded by saying, " I knew. That's why I let you beat me. " That evening at 8:00 pm, the President addressed the country regarding the developing crisis. One hundred million Americans sat in front of their TVs and radios to listen to the speech. This number represented the largest number of Americans to ever to hear a Presidential address. As Kennedy spoke, 22 US Air Force planes turned toward Cuba, in case the response to his speech was an attack. In his speech, Kennedy announced the " quarantine" , and demanded that the missiles be removed. He stated "that if they were not [removed]", further actions would be taken.

Immediately, 56 American warships steamed into their positions to enforce the blockade. All military leaves were cancelled, and US forces were placed on a DEFCON-3 alert. Plans proceeded and troops began massing for an attack on Cuba. The Organization of American States met and voted unanimously to condemn the Soviet actions, and to demand the removal of Soviet missiles. The world stood still. It seemed that nuclear war was a very real possibility.

On Wednesday, as the blockade went into effect, word was received that a number of Russian ships had stopped in mid-sea. Rusk said to Bundy: " We"re eyeball to eyeball, and I think the other fellow just blinked. " But while the Soviets turned their ships around, work was continuing on the missile sites themselves. And Khrushchev's initial responses were not promising. He made it clear, however, that he was not interested in initiating thermo-nuclear war. But time was running out. Air strikes were scheduled for the morning of October 30th. A series of messages passed back and forth between Kennedy and Khrushchev. Some of the messages were more belligerent and some less so. It looked like an agreement could be reached, but no one was quite sure.

Finally, on the morning of October 28th, Moscow radio announced that there would be an important message that evening, Moscow time. At 9:00 AM, they read the text of a letter that Premier Khrushchev was sending President Kennedy: " In order to complete with greater speed the liquidation of the conflict dangerous to the cause of peace, to give confidence to all people longing for peace, and to calm the American people, who, I am certain, want peace as much as the people of the Soviet Union, the Soviet Government, in addition to previously issued instructions on the cessation of further work at building sites for the weapons, has issued a new order on the dismantling of the weapons which you describe as " offensive, " and their crating and return to the Soviet Union. " 

The crisis was over; the Soviets had backed down. They really had been given no choice. Later information was to show that the Soviets only had 20 inaccurate Ballistic missiles and 155 heavy bombers pointed towards the United States, while the United States had 156 ICBM, 144 Polaris missiles, and 1,300 bombers ready to strike. The United States subsequently agreed to withdraw its medium-range missiles from Turkey. The world had come closer to a nuclear war than any time before or since. By all accounts, Kennedy did a superb job of navigating this crisis. He heard various parties and opinions and set course on a response that allowed Khrushchev to back down, while not endangering the vital interests of the US.