In November 1961 William Harvey was ordered to activate an assassination plot against Fidel Castro. This became part of what became known as the ZR/RIFLE project. Harvey decided to transfer David Sanchez Morales from Mexico City to the JM WAVE station. Johnny Roselli was also recruited into the project.

Roselli persuaded Santos Trafficante, the senior Mafia figure in Cuba, to join the conspiracy. Meyer Lansky also became involved in this plot and was reportedly offering a million-dollar reward for the Cuban leader's murder. Richard Cain, a specialist in electronics and wire taps, was also recruited by Roselli. Cain took part in a failed attempt in March 1961 to poison Castro.

On 12th March, 1961, William Harvey arranged for CIA operative, Jim O'Connell, to meet Sam Giancana, Santo Trafficante, Johnny Roselli and Robert Maheu at the Fontainebleau Hotel. During the meeting O'Connell gave poison pills and $10,000 to Rosselli to be used against Fidel Castro. As Richard D. Mahoney points out in his book, Sons and Brothers, The days of Jack and Bobby Kennedy (1999): "Late one evening, probably March 13, Rosselli passed the poison pills and the money to a small, reddish-haired Afro-Cuban by the name of Rafael "Macho" Gener in the Boom Boom Room, a location Giancana thought "stupid." Rosselli's purpose, however, was not just to assassinate Castro but to set up the Mafia's partner in crime, the United States government. Accordingly, he was laying a long, bright trail of evidence that unmistakably implicated the CIA in the Castro plot. This evidence, whose purpose was blackmail, would prove critical in the CIA's cover-up of the Kennedy assassination."

During the Cuban Missile Crisis, Robert Kennedy instructed CIA director John McCone, to halt all covert operations aimed at Cuba. A few days later he discovered that William Harvey had ignored this order and had dispatched three commando teams into Cuba to prepare for what he believed would be an inevitable invasion. Kennedy was furious and as soon as the Cuban Missile Crisis was over, Harvey was removed as commander of ZR/RIFLE. On 30th October, 1962, RFK terminated "all sabotage operations" against Cuba. As a result of President Kennedy's promise to Nikita Khrushchev that he would not invade Cuba, Operation Mongoose was disbanded.