Soon after the success of the Cuban Revolution, militant counter-revolutionary groups developed in an attempt to overthrow the new regime. Undertaking armed attacks against government forces. On 3 April 1961, a bomb attack on militia barracks in Bayamo killed four militia, and wounded eight more.
The Cuban security apparatus knew the invasion was coming, via their extensive secret intelligence network. Nevertheless, days before the invasion, multiple acts of sabotage were carried out, such as the El Encanto fire, an arson attack in a department store in Havana on 13 April that killed one shop worker.
During the night of 14/15 April, a diversionary landing was planned near Baracoa, Oriente Province, by about 164 Cuban exiles commanded by Higinio 'Nino' Diaz.The reconnaissance boats turned back to the ship after their crews detected activities by Cuban militia forces along the coastline. As a result of those activities, at daybreak, a reconnaissance sortie over the Baracoa area was launched from Santiago de Cuba. That was a FAR (Fuerza Aérea Revolucionaria) (Cuban Air Force) T-33, piloted by Lt Orestes Acosta, and it crashed fatally into the sea.
On April 15,The Cuban national police, led by Efigenio Ameijeiras, started the process of arresting thousands of suspected anti-revolutionary individuals, and detaining them in provisional locations such as the Karl Marx Theatre, the moat of Fortaleza de la Cabana and the Principe Castle all in Havana, and the baseball park in Matanzas.
The CIA and the Democratic Revolutionary Front had based a 1,400-strong army, Brigade 2506, in Nicaragua. On the night of 16 to 17 April, Brigade 2506 landed along Cuba's Bay of Pigs and engaged in a firefight with a local revolutionary militia .
During the night of 16/17 April, a mock diversionary landing was organized by CIA operatives near Bahía Honda, Pinar del Río Province. A flotilla containing equipment that broadcast sounds and other effects of a shipborne invasion landing provided the source of Cuban reports that briefly lured Fidel Castro away from the Bay of Pigs battlefront area.
On April 17, 1961, 1,400 U.S.-trained Cuban exiles invaded Cuba during the Bay of Pigs Invasion. Guevara did not play a key role in the fighting, as one day before the invasion a warship carrying Marines faked an invasion off the West Coast of Pinar del Río and drew forces commanded by Guevara to that region.
During the night of 17–18 April, the force at Red Beach came under repeated counter-attacks from the Cuban Army and militia. As casualties mounted and ammunition was used up, the brigadistas steadily gave way. Airdrops from four C-54s and 2 C-46s had only limited success in landing more ammunition.
As the men from Red Beach arrived at Girón, San Román and Oliva met to discuss the situation. With ammunition running low, Oliva suggested that the Brigade 2506 retreat into the Escambray mountains to wage guerilla warfare, but San Román decided to hold the beachhead.
By April 19, 1961, the Cuban government had captured or killed the invading exiles, and Kennedy was forced to negotiate for the release of the 1,189 survivors. Twenty months later, Cuba released the captured exiles in exchange for $53 million worth of food and medicine.
The final air attack mission (code-named Mad Dog Flight) comprised five B-26s, four of which were manned by American CIA contract aircrews and volunteer pilots from the Alabama Air Guard. One FAR Sea Fury (piloted by Douglas Rudd) and two FAR T-33s (piloted by Rafael del Pino and Alvaro Prendes) shot down two of these B-26s, killing four American airmen. Combat air patrols were flown by Douglas A4D-2N Skyhawk jets of VA-34 squadron operating from USS Essex, with nationality and other markings removed. Sorties were flown to reassure Brigade soldiers and pilots, and to intimidate Cuban government forces without directly engaging in acts of war.
Late on 19 April, destroyers USS Eaton (code-named Santiago) and USS Murray (code-named Tampico) moved into Cochinos Bay to evacuate retreating Brigade soldiers from beaches, before fire from Cuban army tanks caused Commodore Crutchfield to order a withdrawal.
On 20 April, Humberto Sorí Marin was executed at Fortaleza de la Cabaña, having been arrested on 18 March following infiltration into Cuba with 14 tons of explosives. His fellow conspirators Rogelio González Corzo (alias "Francisco Gutierrez"), Rafael Diaz Hanscom, Eufemio Fernandez, Arturo Hernandez Tellaheche and Manuel Lorenzo Puig Miyar were also executed.
Castro ordered Captain José Ramón Fernández to launch the counter-offensive, before taking personal control of it. After bombing the invaders' ships and bringing in reinforcements, Castro forced the Brigade to surrender on 20 April.
On 21 April, Eaton and Murray, joined on 22 April by destroyers USS Conway and USS Cony, plus submarine USS Threadfin and a CIA PBY-5A Catalina flying boat, continued to search the coastline, reefs, and islands for scattered Brigade survivors, about 24–30 being rescued.