On Tuesday, May 30, 1961 Trujillo was shot and killed when his blue Chevrolet Bel Air was ambushed on a road outside the Dominican capital. He was the victim of an ambush plotted by a number of men among them Antonio de la Maza, Amado García Guerrero, and General Antonio Imbert Barrera. The plotters, however, failed to take control as the later-to-be-executed General José ("Pupo") Román betrayed his co-conspirators by his inactivity, and contingency plans had not been made. On the other side, Johnny Abbes, Roberto Figueroa Carrión, and the Trujillo family put the SIM to work to hunt down the members of the plot and brought back Ramfis Trujillo from Paris to step into his father's shoes. The response by SIM was swift and brutal. Hundreds of suspects were detained, many tortured. On November 18 the last executions took place when six of the conspirators were executed at the "Hacienda Maria Massacre". Imbert was the only one of the seven assassins who survived the manhunt.
Trujillo's funeral was that of a statesman with the long procession ending in his hometown of San Cristóbal, where his body was first buried. President Joaquín Balaguer gave the eulogy. The efforts of the Trujillo family to keep control of the country ultimately failed. A military uprising in November and the threat of American intervention set the final stage and ended the Trujillo regime. Ramfis tried to flee with his father's body upon his boat Angelita, but was turned back. Balaguer allowed Ramfis to leave the country and to relocate his father's body to Paris. There the remains were interred in the Cimetière du Père Lachaise on August 14, 1964, and six years later moved to the El Pardo cemetery near Madrid, Spain.
The role of the Central Intelligence Agency in the killing has been debated. Imbert insists that the plotters acted on their own. In a report to the Deputy Attorney General of the United States, CIA officials described the agency as having "no active part" in the assassination and only a "faint connection" with the groups that planned the killing. Another internal CIA memorandum states that an Office of Inspector General investigation into Trujillo's murder disclosed "quite extensive Agency involvement with the plotters." The weapons of the assassins included three M1 carbines that had been supplied by the CIA.
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