He enlisted in the U.S. Army on October 23, 1945, at Springfield, Massachusetts as a private, eventually becoming part of the Allied Occupation Force in Germany on completion of basic training.

While heading the CIA office (known as "JMWAVE") shortly after the 1961 Bay of Pigs Invasion, Shackley dealt with operations in Cuba (alongside Edward Lansdale).

During this period as Miami Station Chief, Shackley was in charge of about 400 agents and general operatives (as well as a huge flotilla of boats), and his tenure there encompassed the Cuban Missile Crisis of October 1962.

Shackley was responsible for running the Phoenix Program and the Provincial Reconnaissance Units (PRUs), a secret assassination and capture campaign aimed at members of the Viet Cong infrastructure.

[10] According to Thomas Bodenheimer and Robert Gould, Shackley was linked to the Australian Nugan Hand Bank where heroin trade profits worth millions of dollars were transferred to after the Fall of Saigon in 1975.

[2] Reportedly, he was forced out of the CIA by Turner who disapproved of Shackley's involvement with former officer Edwin P. Wilson, who was under federal investigation for smuggling explosives to Libya.

[citation needed] Shackley was suspected by federal prosecutor Lawrence Barcella to be part of Wilson's Egyptian-American Transport and Services Corporation (EATSCO), a front for his arms smuggling which was also accused of fraudulently billing the Department of Defense.

[20][19] Ghorbanifar, known to the CIA as a person of questionable reliability and veracity, attempted to show that he and Hashemi had influence in Iran by stating that the Iranians would be willing to trade captured Soviet equipment for TOW missiles.

[19] Ghorbanifar also proposed that a cash payment be offered as ransom for the four American hostages held in Beirut, Lebanon (which included William Francis Buckley*) and that he act as the intermediary.

)[19] In May 1985, Shackley discussed the hostage issue with Michael Ledeen and shared that he had received no response from Walters regarding the report he had prepared regarding the November meeting with Ghorbanifar.

[22] In June, Shackley prepared an updated second report that outlined a similar proposal from Ghorbanifar in which he suggested a "discussion of a quid pro quo that involved items other than money.

[23] After detailing his encounter with Ghorbanifar in Hamburg and the nature of his reports to the State Department and Ledeen, he wrote: "When anyone asserts that my intervention on behalf of the hostages shows that I must also have participated in the transfer of weapons to Iran and, therefore, must have helped supply the contras with funds, material or arms, I can only gape in amazement and conclude that there are those who have studied logic from a different textbook than I did.

"[23] Shackley concluded his statement: "I was not a participant in the Iran weapons transfer; I was not in the past, nor am I now, involved in providing aid of any kind of the contras; and I completely endorse the position that no U.S. intelligence operation that is in violation of an act of Congress should be undertaken.