Kennedy ran for president in 1960, one of his key election issues was an alleged "missile gap" with the Soviets.
In 1961, America discovered the Soviets had only four R-7 Semyorka intercontinental ballistic missiles (ICBMs).
The USSR issued an ultimatum demanding the withdrawal of all armed forces from Berlin, including the Western armed forces in West Berlin. The crisis culminated in the city's de facto partition with the East German erection of the Berlin Wall.
In late 1961, Fidel Castro asked for more SA-2 anti-aircraft missiles from the Soviet Union. The request was not acted upon by the Soviet leadership.
In early 1962, a group of Soviet military and missile construction specialists accompanied an agricultural delegation to Havana.
In January 1962, US Army General Edward Lansdale described plans to overthrow the Cuban government in a top-secret report (partially declassified 1989), addressed to Kennedy and officials involved with Operation Mongoose.
Timothy Naftali has contended that Escalante's dismissal was a motivating factor behind the Soviet decision to place nuclear missiles in Cuba in 1962.
In February 1962, the US launched an embargo against Cuba, and Lansdale presented a 26-page, top-secret timetable for implementation of the overthrow of the Cuban government.
In May 1962, Soviet First Secretary Nikita Khrushchev was persuaded by the idea of countering the US's growing lead in developing and deploying strategic missiles by placing Soviet intermediate-range nuclear missiles in Cuba.
By May, Khrushchev and Castro agreed to place strategic nuclear missiles secretly in Cuba.
Specialists in missile construction under the guise of "machine operators", "irrigation specialists", and "agricultural specialists" arrived in July.
CIA director John A. McCone was suspicious. Sending antiaircraft missiles into Cuba, he reasoned, "made sense only if Moscow intended to use them to shield a base for ballistic missiles aimed at the United States". On August 10, he wrote a memo to Kennedy in which he guessed that the Soviets were preparing to introduce ballistic missiles into Cuba.
The first issue that led to a pause in reconnaissance flights took place on August 30, when a U-2 operated by the US Air Force's Strategic Air Command flew over Sakhalin Island in the Soviet Far East by mistake.
On August 31, Senator Kenneth Keating (R-New York) warned on the Senate floor that the Soviet Union was "in all probability" constructing a missile base in Cuba. He charged the Kennedy administration with covering up a major threat to the US, thereby starting the crisis.
In September 1962, analysts from the Defense Intelligence Agency (DIA) noticed that Cuban surface-to-air missile sites were arranged in a pattern similar to those used by the Soviet Union to protect its ICBM bases, leading DIA to lobby for the resumption of U-2 flights over the island.
The first consignment of Soviet R-12 missiles arrived on the night of September 8, followed by a second on September 16. The R-12 was a medium-range ballistic missile, capable of carrying a thermonuclear warhead.
On October 15, the CIA's National Photographic Interpretation Center (NPIC) reviewed the U-2 photographs and identified objects that they interpreted as medium range ballistic missiles.
On October 17, Soviet embassy official Georgy Bolshakov brought President Kennedy a personal message from Khrushchev reassuring him that "under no circumstances would surface-to-surface missiles be sent to Cuba."
On October 19, the EXCOMM formed separate working groups to examine the air strike and blockade options, and by the afternoon most support in the EXCOMM shifted to the blockade option.
Kennedy met with members of EXCOMM and other top advisers throughout October 21, considering two remaining options: an air strike primarily against the Cuban missile bases or a naval blockade of Cuba.
On October 22 at 7:00 pm EDT, Kennedy delivered a nationwide televised address on all of the major networks announcing the discovery of the missiles.
At 10:00 pm EDT, the US raised the readiness level of SAC forces to DEFCON 2. For the only confirmed time in US history, B-52 bombers went on continuous airborne alert, and B-47 medium bombers were dispersed to various military and civilian airfields and made ready to take off, fully equipped, on 15 minutes' notice.
On Saturday, October 27, after much deliberation between the Soviet Union and Kennedy's cabinet, Kennedy secretly agreed to remove all missiles set in Turkey and possibly southern Italy, the former on the border of the Soviet Union, in exchange for Khrushchev removing all missiles in Cuba.
Soviet nuclear capability in 1962 placed less emphasis on ICBMs than on medium and intermediate-range ballistic missiles (MRBMs and IRBMs).