How the CIA’s ‘Benign Coverup’ After the JFK Assassination Gave Rise to the ‘Deep State’

The day after Lee Harvey Oswald shot President John F. Kennedy in Dallas in 1963, an FBI agent showed up at the door of Oswald’s mother with a cutout of a man’s image, believing it was her son or an associate.

I got it from the CIA, the agent told her, according to a newly released Central Intelligence Agency document. In doing so, he blew off the one request the agency had made—to keep its name out of it—and helped set off decades of secrets, contortions and coverups that are still being unraveled today.

A cache of 82,864 pages that the Trump administration released this week related to the Kennedy assassination lay bare the extent to which the CIA tried to hide what it knew from the very day Kennedy was shot, and how its clumsy efforts fed dangerous suspicions about the agency and the nature of the American government.

As waves of hysteria shook the country in the aftermath of the assassination, the story of the photo took on a life of its own. Why was the CIA monitoring Kennedy’s assassin just months before he killed the president? As a series of investigations proceeded, CIA officials would give wildly divergent accounts of the photo, leading a small part of the public to consider an idea that had previously been nearly taboo in America: What if elements of the government itself conspired to take over?

Two months before the assassination, the CIA had photographed Oswald in Mexico City, where he tried to get visas from the Cubans and Russians.

What the CIA was trying to protect by distancing itself from the photo was its vast gauntlet of surveillance of Soviet and Cuban diplomatic missions in Mexico City. The surveillance included a microphone in a coffee-table leg in the Cuban ambassador’s office, “six base houses commanding the entrances to target embassies, two mobile photosurveillance trucks and three agents trained in photo surveillance on foot.”

In the decades to come, the CIA would attempt again and again to hide from Kennedy investigators far darker truths about how it operated overseas, including its wielding of terrorism against enemies, its use of Mafia hit men and attempts to rig foreign elections.

But the revelations came out anyway, and each time they did, the flames were fanned of a once fringe belief of a secret Washington cabal. It metastasized into an idea so compelling that it would become the central plank of an American presidency 60 years later.

“The Kennedy Assassination and the conspiracy that grows out of it are at the root of what people now refer to as the ‘deep state,’ ” said Steven Gillon, a Kennedy historian.

One of President Trump’s most consistent narratives since his first term has been that a conspiracy of intelligence operatives, bureaucrats, and media cohorts have tried to usurp the voters’ will and thwart him, including by drumming up false prosecutions. “With you at my side, we will demolish the deep state. We will expel the warmongers,” he said at an event sponsored by the Conservative Political Action Conference in 2023. “I will fire the unelected bureaucrats and shadow forces.”

Within three days of taking office in January, he ordered the release of the remaining JFK documents. “It’s been 60 years, time for the American people to know the TRUTH!” Trump wrote in his executive order.

The latest documents, mostly comprising faded typewritten text and some handwritten notes, shed new light on the conduct of the CIA in the years immediately before and after the assassination, underscoring the giant sweep of its operations.

One document revealed the CIA placed “chemical contaminating agent in Cuban sugar bound for the Soviet Union.” Another showed that CIA operatives, with the help of the American Mafia, agreed to attempt to kill Cuban leader Fidel Castro for $100,000, and pay $20,000 each for the assassination of Castro’s brother, Raúl Castro, and Che Guevara, a hero in the Communist world.

A third document released this week—a memo from Kennedy aide Arthur Schlesinger Jr. to his boss—warned that intelligence operatives were growing too powerful, using language that a contemporary Trump supporter might appreciate. While the U.S. had 3,700 diplomats overseas, the CIA also had some 1,500 officers pretending to work under State Department cover at the time. “The contemporary CIA possesses many of the characteristics of a state within a state,” he wrote.

Castro’s revenge

The CIA photo shown to Oswald’s mother led to public revelations about other surveillance the agency had of the assassin’s contact with Cuban officials in Mexico City. That led to more questions about CIA operations against Cuba. Just two months before the assassination, Castro warned that if the U.S. tried to kill “Cuban leaders, they themselves will not be safe.” Could Castro have been trying to get revenge?

The CIA later revealed it had engaged in what it described as a “benign coverup” concealing from JFK investigators its efforts to topple the Cuban government. Agency officials would later say it wanted to lead investigators toward the “best truth” that Oswald was a lone gunman with no foreign backing; CIA officials feared candor about its own activities could have led investigators to the conclusion that Castro had killed Kennedy out of revenge, triggering a catastrophic conflict with the Soviet Union.

By the 1980s, polling showed that most Americans believed Washington had a role in the Kennedy assassination, according to Gillon, the Kennedy historian. One of the most popular theories was a dark mirror of American actions in Cuba: that the CIA had worked in concert with defense contractors, anti-Castro groups and Mafia figures to kill Kennedy.

In the past, most American conspiracy theories pointed to foreign nations secretly trying to subvert the U.S. But revelations that the CIA was capable of deploying Mafia hit men to other countries to kill a president in a neighboring country fueled concerns that it could be trying to do so at home. “It’s not a huge intellectual leap that if we are doing this abroad we might do it on our own shores as well,” said Jonathan Earle, a Louisiana State University historian who has studied the growth of American conspiracy theories.

That theory went mainstream in Oliver Stone’s 1991 blockbuster “JFK,” whose protagonist declares “President Kennedy was murdered by a conspiracy that was planned in advance at the highest levels of our government.” The character exhorts viewers that the proof is tucked away in the government’s hidden files. “All these documents are yours. The people’s property. You pay for it.”

At the end of the film, a text screen calls on viewers to contact their lawmakers to demand the release, and many did.

The following year, Congress passed the JFK Records Act mandating that assassination related materials be released by 2017. In the intervening decades the CIA repeatedly argued that some of the releases would hurt its operations. As documents were released with heavy redactions, they seemed to confirm suspicions among the public that the government was still hiding something about Kennedy’s killing.

By 2017, Trump was in his first term in office but already mired in accusations from the intelligence community that his campaign was assisted by Russia. His claims that a deep state was trying to undermine him—and by extension the American public—began to merge with theories about Kennedy’s assassination.

Trump’s promotion of the idea of a deep state has converted many on the right to the belief that the government played a role in Kennedy’s assassination, said Gerald Posner, author of “Case Closed,” a book debunking the conspiracy theories associated with JFK. “It’s an article of faith that what happened to Trump is a ‘deep-state’ operation,” said Posner, describing the thinking, adding: “That’s what the deep state does. It eliminates and destroys presidents it doesn’t like.”

Write to Joel Schectman at joel.schectman@wsj.com and Brian Whitton at brian.whitton@wsj.com