President John F. Kennedy did not react with common sense to the U.S. defeat at the Bay of Pigs. He sought revenge. The Taylor Commission, established by the President to analyze the fiasco, recommended initiating new political, military, economic and propaganda measures "against Castro." The report led to the preparation and implementation of a new undercover operations plan, known as Operation Mongoose, which beginning in November 1961 unleashed thousands of terrorist acts, sabotage, assassination attempts and armed attacks.

Some months later, General Maxwell D. Taylor, at that time serving as head of the Joint Chiefs of Staff, told the President that he did not think it would be possible to overthrow the Cuban government without a direct U.S. intervention and recommended a "more aggressive" course of action than Operation Mongoose. He proposed an escalation of the operations authorized by Kennedy to create an incident which could precipitate a massive surprise air attack and/or invasion.

On March 7, 1962, the Joint Chiefs of Staff proposed "creating a provocation which would justify U.S. military action" and just two days later, the Secretary of Defense submitted to the Joint Chiefs of Staff a set of measures designed to serve as the pretext for such an intervention in Cuba.

Amidst the escalating tension orchestrated by the United States, on May 29, 1962, a Soviet delegation, led by a member of the Communist Party Central Committee Presidium, arrived in Cuba with a proposal to install ballistic nuclear missiles on the island, in order to protect the country from U.S. invasion and strengthen the world’s socialist positions.

The leadership of the Revolution and the Soviet government signed an agreement establishing military collaboration in the defense of Cuba’s national territory. Despite the fact that the agreement was totally within the boundaries of international law and its signing was a prerogative of sovereign states, the Soviet leadership did not accept the Cuban proposal to make the decisions public, which served as a pretext for the Kennedy administration to precipitate a crisis.

On June 20, 1962, the Soviet General Staff approved the assignment of officers and troops for Operation Anadyr. Commandante Raúl Castro went to Moscow July 3-16 to announce the Cuban-Soviet agreement as a sovereign agreement between the two nations. Nevertheless, the Soviets insisted on keeping the operations secret, which was not possible given their magnitude and the continual U.S. reconnaissance flights over Cuban territory.

Soviet troops began to arrive in Cuba during the first week of August. U.S. intelligence had already detected anti-aircraft missiles, MIG-21 aircraft and unidentified constructions, as well as the presence of Soviet military experts. On October 16, the United States U-2’s confirmed ballistic nuclear missile bases in

San Cristóbal, Pinar del Río province and on this same day, around 11:00am, Kennedy convened a meeting of officials who would later become the Executive Committee of the National Security Council. The group studied various proposals for action over the course of five days and on October 20, decided to impose a "naval blockade" on Cuba, for which five task forces were established.

Beginning on October 21, U.S. Armed Forces were moved from the status of peacetime defense (DEFCON–5) to high alert (DEFCON–3) and ordered to relocate anti-aircraft forces to prepare for combat, reinforce the U.S. Naval Base at Guantánamo, evacuate families and civilians from the base, and deploy the forces necessary to impose the blockade.

On October 22, with the U.S. naval blockade in place and the mobilization of forces to bomb or invade Cuba, the so-called Missile Crisis unfolded. Kennedy demanded the withdrawal of Soviet strategic weapons from Cuba and announced the naval blockade to which the Revolutionary Armed Forces responded with a combat alert for all units and a popular mobilization to confront the possibility of an invasion of gigantic proportions that could unleash a nuclear holocaust.

U.S. reconnaissance flights increased to such an extent that, on October 26, Fidel ordered that, the following day, enemy aircraft flying at low altitudes be fired upon. Given the insolence of the U.S. government, a U-2 was downed with an anti-aircraft missile over Oriente province on October 27, one of the most charged moments during the crisis.

October 26th through the 31st, there was an exchange of messages between Nikita Khrushchev and Fidel. Those sent by Khrushchev made clear the unilateral manner in which the Soviets were acting and their underestimation of Cuba, while those of Fidel warned of the imminent dangers and expressed Cuba’s commitment to revolutionary principles.

On Sunday, October 28, the Kremlin communicated to Washington that orders had been given to halt construction of missile bases in Cuba, to dismantle those in existence and return the nuclear missiles to the USSR. The U.S. responded with a demand to inspect Cuban territory to verify the operations. That afternoon, Cuba rejected the inspection which the two super-powers had agreed to and announced its five point position.

The United States and the Soviet Union reached an agreement based on a proposal made by Khrushchev on October 26 and the U.S. inspected the weapons aboard Soviet ships outside of Cuban territorial waters, which for the two super-powers marked the end of the crisis. The naval blockade was suspended October 30 and 31, for a visit by United Nations General Secretary U. Thant to Cuba, and re-established November 1. At 6:45 pm on November 20, Kennedy ordered the lifting of the blockade and on the 22nd the Revolutionary government declared a return to normalcy on the island, on war footing since October 22.