After Frank Wisner suffered a mental breakdown in September 1958, Bissell replaced him as the CIA's Deputy Director for Plans. Bissell assumed the office on 1 January 1959. He was meanwhile also playing a key role as CIA Program Manager in the development of the Corona program.
Leading the CIA's Directorate of Plans (DDP) put Bissell in a vital position. The DDP branch of the CIA was responsible for covert operations, such as the prior overthrow of Mohammad Mosaddegh and Jacobo Árbenz. When Bissell took office, the main DDP target was Fidel Castro.
In March 1960, a top-secret policy paper, titled "A Program of Covert Action Against the Castro Regime" (code-named JMARC), was drafted "to bring about the replacement of the Castro regime with one more ... acceptable to the U.S. in such a manner as to avoid any appearance of U.S. intervention." The courses of action outlined in the paper were based on Operation PBSuccess, which had worked to great effect in Guatemala in 1954. In fact, Bissell assembled the same team as the one used in Guatemala: Tracy Barnes, David Atlee Phillips, Jacob Esterline, William "Rip" Robertson, E. Howard Hunt and Gerry Droller (aka "Frank Bender"). Added to the team were Lieutenant Colonel Jack Hawkins, Desmond FitzGerald, William Harvey and Ted Shackley.