Conspiracy theory suggests that a secret or shadow government including wealthy industrialists and right-wing politicians ordered the assassination of Kennedy. People say that Kennedy's death allowed for policy reversals desired by the secret government to escalate the United States military involvement in Vietnam.

CIA agent David Atlee Phillips, using the pseudonym "Maurice Bishop", was involved with Oswald prior to the Kennedy assassination in connection with anti-Castro Cuban groups.CIA and FBI deliberately tampered with their files on Lee Harvey Oswald both before and after the assassination. Kennedy's relationship with the CIA was strained considerably following the failed Bay of Pigs Invasion. He remarked that he wanted "to splinter the CIA into a thousand pieces and scatter it to the winds."

The House Select Committee on Assassinations reported:
No actions were taken by the agent in the right front seat of the Presidential limousine Roy Kellerman to cover the President with his body, although it would have been consistent with Secret Service procedure for him to have done so. The primary function of the agent was to remain at all times in close proximity to the President in the event of such emergencies.
Vince Palamara, who interviewed several Secret Service agents assigned to the Kennedy detail, disputes this. Palamara reports that Secret Service driver Sam Kinney told him that requestssuch as removing the bubble top from the limousine in Dallas, not having agents positioned beside the limousine's rear bumper, and reducing the number of Dallas police motorcycle outriders near the limousine's rear bumperwere not made by Kennedy.
Kennedy alienated Southerners and conservatives around the country, most of whom were already suspicious of him. In this, the Secret Service reflected the more backward elements of America. Many of the agents with whom I worked were products of the South.... I heard some members of the White House detail say that if shots were fired at the president, they'd take no action to protect him. A few agents vowed that they would quit the Secret Service rather than give up their lives for Kennedy.

People believed that the Cuban government was a suspect in the assassination of JFK. People said that Fidel Castro had ordered the assassination due to the CIA apparently trying to assassinate Castro.