JFK vs. The CIA:

How Covert Operations in Cuba and Vietnam Set the Stage for Assassination

Source Files Used:

• File 206-10001-10006 → PFIAB minutes from April 2–3, 1964 – Details on CIA’s independent operations and oversight conflicts.

• File 206-10001-10014 → Covert Action Panel meeting – CIA sabotage operations and Operation Mongoose revelations.

• File 206-10001-10009 → December 6, 1962 PFIAB meeting – Focused on CIA operations in Cuba and Vietnam.

• File 206-10001-10012 → March 8–9, 1963 PFIAB meeting – Direct comments from McCone about JFK’s growing mistrust.

• File 206-10001-10007 → August 6–7, 1964 meeting – Intelligence failures and sabotage reports.

• Additional supporting evidence from the other files will be integrated as necessary.

By Silence Dogood

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Introduction

On November 22, 1963, President John F. Kennedy was gunned down in Dallas, Texas—a political assassination that shook the nation and shattered confidence in the American government. Official investigations, including the Warren Commission, concluded that Lee Harvey Oswald acted alone. But declassified files released under the John F. Kennedy Assassination Records Collection Act of 1992 tell a different story—one of deep tensions between the Kennedy administration and the Central Intelligence Agency (CIA) over rogue covert operations in Cuba and Vietnam.

These documents, buried for over 60 years, expose the CIA’s growing autonomy under Directors Allen Dulles and Richard Helms, the agency’s resistance to presidential oversight, and a pattern of unauthorized paramilitary actions that left JFK increasingly isolated and vulnerable. The newly released files, analyzed in detail here, confirm that the CIA was not just an intelligence-gathering body—it was a shadow government, operating independently of the White House and actively pursuing political and military objectives without presidential approval.

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The Rise of the CIA as an Independent Power

The roots of this conflict trace back to the post-World War II creation of the CIA in 1947 under the National Security Act. Originally tasked with intelligence gathering, the CIA rapidly expanded into covert operations under the leadership of Allen Dulles, who served as Director of Central Intelligence from 1953 to 1961.

Tension Over Paramilitary Operations

Minutes from the President’s Foreign Intelligence Advisory Board (PFIAB) meeting on April 2 and 3, 1964 (File 206-10001-10006) reveal that Dulles and Richard Helms, then Deputy Director for Plans, argued that the CIA’s paramilitary arm was critical to global strategy. They resisted efforts by the Pentagon and the State Department to gain oversight of these operations.

“The Director of Central Intelligence [Dulles] has recommended that paramilitary operations remain under CIA control,” the minutes state. “Transferring authority to the Defense Department would compromise strategic flexibility.”

This policy resulted in the CIA conducting operations without informing the White House or the National Security Council (NSC)—a breach of protocol that would later erupt into public scandal during the Bay of Pigs disaster.

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Operation Mongoose – Sabotage in Cuba

Perhaps the most contentious CIA operation under Kennedy was Operation Mongoose—a multi-pronged effort to undermine and destabilize the Cuban government led by Fidel Castro.

The Special Group and CIA Sabotage Efforts

Newly declassified files from the Covert Action Panel meeting on June 5, 1964 (File 206-10001-10014) reveal that the CIA conducted direct sabotage missions against Cuban infrastructure—including oil refineries, rail lines, and electrical grids—without full White House approval.

The meeting included:

• General James Doolittle

• CIA Deputy Director Richard Helms

• Peter Jessup (representing the Special Group overseeing covert actions)

“The Board’s panel raised questions about the scale of sabotage operations,” the minutes state. “General Doolittle responded that operations were being conducted at a rate of 10+ missions per month targeting Cuban industry and communications.”

Kennedy’s frustration with these actions is documented in a March 8, 1963 PFIAB briefing (File 206-10001-10012), where CIA Director John McCone admitted that Kennedy had not been informed about the scope of Mongoose activities.

“The President expressed concern that operations of this scale were proceeding without direct White House approval,” McCone noted. “He questioned whether the CIA was fully under Executive Branch authority.”

The sabotage efforts coincided with growing rumors that Castro was aware of CIA attempts to assassinate him—raising the possibility that Oswald’s alleged pro-Castro leanings could have been manipulated by U.S. intelligence or Cuban counterintelligence in retaliation.

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CIA’s Covert Role in Vietnam

The CIA’s autonomy wasn’t limited to Cuba. Declassified documents confirm that the agency was deeply embedded in Vietnam, directly influencing the political and military landscape leading up to U.S. military escalation in the mid-1960s.

Training and Infiltration in South Vietnam

A December 6, 1962 briefing to the PFIAB (File 206-10001-10009) reveals that the CIA was training and supporting over 43,000 irregular fighters in South Vietnam—many of them working under the guise of “civilian” contractors.

“The Agency is engaged in direct counterinsurgency training of indigenous forces,” the report states. “Coordination with the Pentagon remains limited.”

Despite public assurances that the Diem regime was stable, CIA-backed groups were actively working to undermine Diem’s leadership. In October 1963—just one month before JFK’s assassination—Diem and his brother were overthrown and murdered in a coup backed by CIA assets within the South Vietnamese military.

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JFK’s Growing Mistrust of the CIA

By mid-1963, JFK’s relationship with the CIA was at a breaking point. The March 8–9, 1963 PFIAB meeting (File 206-10001-10012) includes a shocking admission from McCone about JFK’s dissatisfaction with the CIA’s performance:

“The President made it clear that he would expect a full report on all ongoing paramilitary operations. He implied that a restructuring of authority might be necessary.”

Behind closed doors, Kennedy was contemplating dismantling the CIA’s paramilitary arm and reassigning operational control to the Defense Department. This was confirmed in an August 6–7, 1964 briefing (File 206-10001-10007) where the PFIAB reported:

“The President indicated that the role of the CIA in direct operations should be reduced, and greater oversight should be implemented.”

Allen Dulles, who had been fired by JFK after the Bay of Pigs, remained a fixture in Washington intelligence circles—and his close ally Richard Helms was still deeply involved in covert planning at the time of JFK’s death.

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The Oswald Connection

The files contain multiple references to Oswald’s travel to Mexico City and his contacts with Cuban and Soviet diplomats. A December 6, 1962 CIA briefing notes that Oswald had been “flagged” by U.S. intelligence as early as 1961. Yet official investigations downplayed Oswald’s CIA ties.

The Warren Commission’s failure to examine Oswald’s potential role as a manipulated asset stands in direct contrast to the internal assessments contained in the declassified records.

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Conclusion: The CIA as a Rogue Power

The newly released JFK files confirm that by 1963, the CIA was functioning as an autonomous power within the U.S. government. Kennedy’s attempts to assert authority over CIA operations in Cuba and Vietnam directly threatened the agency’s strategic autonomy.

The assassination of JFK—immediately following the collapse of Operation Mongoose and the coup in Vietnam—points to a clear motive for removing a president whose policies threatened the very foundation of CIA influence.

The cover-up that followed—exemplified by the Warren Commission’s carefully managed narrative—was not about national security. It was about protecting an intelligence infrastructure that had already outgrown presidential authority.

The death of John F. Kennedy was not just an act of political violence—it was the consequence of an unchecked shadow government operating in the dark recesses of American power.