24) The man who asked too many JFK questions

Charles and Cynthia Thomas
Charles and Cynthia Thomas with one of their children (Credit: Cynthia Thomas)

The late Charles Thomas belonged to an exclusive, unhappy and forgotten club: U.S. government officials whose efforts to honestly investigate the assassination of President John F. Kennedy in 1963 cost them their jobs and reputations.


Last week the Washington Post ran an obituary of Cynthia Thomas, the widow of Charles Thomas. It was an unusual tribute. The Post now acknowledges that there are good and solid reasons for perfectly sane people to reject the U.S. government’s implausible and widely disbelieved official theory that a “lone gunman” killed JFK for no discernible reason.

This is a welcome and overdue development, as the facts of Thomas’s tragic story attest.

Charles Thomas
Charles Thomas, doomed diplomat

Thomas, a Foreign Service officer, was stationed in Mexico from 1964 to 1967. In the course of his consular duties, Thomas gathered first-hand information from credible sources about the visit of accused assassin Lee Harvey Oswald to Mexico City six weeks before JFK’s assassination. Thomas assumed that the CIA and FBI would be interested in his new evidence. He assumed wrong.

In fact, Thomas was punished for asking questions about JFK’s assassination. Despite glowing job recommendations, he was inexplicably dismissed from the Foreign Service in 1969. “It was nonsensical,” Cynthia Thomas told a reporter, “Charles was the best sort of American diplomat.”

Two years later, Charles Thomas put a gun to his right temple in the second-floor bathroom of the couple’s home in northwest Washington and pulled the trigger.


Other than its violent end, Thomas’s story resembles that of John Whitten, a senior CIA official, who died in 2000. Whitten too paid a price for asking JFK questions.

In 1963 Whitten served as chief of the Mexico desk in the clandestine service. He came up through the agency’s Berlin base where he pioneered the use of the polygraph in counterespionage investigations. He investigated the famous case of Otto John, the West German intelligence chief who defected to East Germany in the 1950s.

The day after JFK was killed, deputy CIA director Richard Helms put Whitten in charge of collating all reports on Oswald. Arrested for killing Kennedy, Oswald denied responsibility and told reporters he was “a patsy.” Oswald was then killed in police custody.

The more Whitten learned about Oswald’s Cuban contacts, the more he wanted to investigate. With a clerical staff of 30, he launched a counterespionage investigation of Oswald, a leftist who had lived in the Soviet Union.

John Whitten
John Whitten: His Oswald investigation was also killed

Within a month, Whitten was, in his own words, “sandbagged” by CIA counterintelligence chief James Angleton.

“Angleton started to criticize my report terribly without pointing out any inaccuracies,” Whitten told Senate investigators in closed-door testimony. “It was so full of wrong things, we could not possibly send it to the Bureau, and I just sat there and I did not say a word. This was a typical Angleton performance. I had invited him to comment on the report, and he had withheld all of his comments until he got to the meeting. ”

A legendary and controversial figure in the annals of the CIA, Angleton is best-known for the “mole hunt,” his ceaseless unsuccessful effort to find a Soviet spy inside the CIA in the late 1960s. As I recounted in my 2017 biography of Angleton, The Ghost, Angleton and his molehunters closely monitored Oswald’s travels, foreign contacts and political activities from November 1959 to November 1963.

At a bitter meeting on Christmas Eve 1963, Whitten was relieved of his duties. “Helms wanted someone to conduct the investigation who was in bed with the FBI,” Whitten. “I was not, and Angleton was.”

The questions Whitten wanted to pursue about Oswald and the Cubans were never asked, much less answered, by the Warren Commission, which concluded predictably that Oswald acted alone, and that no one in the government was to blame.

When Whitten, an outstanding undercover officer, received a poor job evaluation in 1965, he quit the CIA and moved to Europe to join the Vienna Men’s Choir.


Thomas and Whitten’s story also resembles that of Win Scott, the veteran chief of the agency’s Mexico station in the 1960s.

As told in my 2008 biography, Our Man in Mexico, Scott and his deputy Ann Goodpasture launched their own private investigation of Oswald at the same time as Thomas. Like Thomas, Scott came to reject the official theory of a “lone gunman.” He wrote as much in an unpublished memoir in 1970.

Our Man in Mexico
Biography of the silenced station chief.

Angleton suppressed Win Scott’s JFK dissent too. When Scott died suddenly in April 1971, Angleton flew to Mexico City and seized Scott’s unpublished manuscript. It would be 20 years before portions of Scott’s memoir surfaced with its damaging account of how the CIA had fed a lie to the Warren Commission about Oswald.

CIA officials then disparaged Scott, who had received the agency’s Distinguished Intelligence Medal in 1969. One CIA official said Scott had “gone to seed.”


Unwelcome Questions

For Thomas’s obituary, the Post turned to an outside writer, former New York Times reporter Philip Shenon. The author of two well-reported books about the Warren Commission and 9/11 Commission, Shenon reported Thomas’s story for The Guardian last spring.

Phil Shenon
Phil Shenon,

In the Post, Shenon wrote:

Declassified government files released in the 1990s suggested to her and her family — and to some historians and researchers who have studied the case — that her husband’s career was ended to stop him from continuing to raise unwelcome questions inside the government about the 1963 assassination of President John F. Kennedy: specifically, about whether the assassin Lee Harvey Oswald had accomplices in Mexico,

Thomas’s “unwelcome questions,” Shenon contends, concerned a possible Cuban communist conspiracy to kill Kennedy.

The long-classified State Department and CIA documents show that her husband alarmed his superiors in the late 1960s by pressing for a new investigation that might have pointed to a conspiracy in Kennedy’s death. It was a plot, he suspected, that had been hatched on Mexican soil and somehow involved officials of the communist government of Cuba.

The implication of the Post’s obituary is that the U.S. government protected Fidel Castro from credible evidence of Cuban involvement in JFK’s assassination–and continues to protect the Cuban government to this day.

As I explain in this piece for Salon, the “Castro did it” theory lacks plausibility.

Why would the CIA protect the impudent revolutionary leader who loved baiting the U.S. government as “Yanqui imperialists” and “war criminals”? The U.S. government had–and has–a policy of unremitting hostility toward the government of Cuba. The agency mounted scores, if not hundreds, of conspiracies to assassinate Castro. Declared U.S. policy long called for the overthrow of Castro’s government.

If Thomas’s evidence credibly pointed to Cuban involvement, why wouldn’t U.S. officials have pursued it, publicized it in order to discredit Castro, facilitate the overthrow of his government, and do justice for the slain president?

To protect themselves is the obvious answer. But what did the CIA have to hide?

CIA Animus

The evidence gathered by Charles Thomas did not necessarily point to a communist conspiracy. It also pointed to the CIA’s knowledge of Oswald.

The myth of the lone gunman notwithstanding, the ex-Marine Corps radio operator was a person of deep and abiding interest to Angleton and other top officers when he visited Mexico in September 1963, six weeks before JFK was killed.

Thomas’s “unwelcome questions” threatened to expose what these officers knew about the supposed “lone nut” while JFK was alive.

The CIA, for example, told the Warren Commission that the Mexico City station did not even know that Oswald had visited the Cuban consulate until after JFK’s assassination.

That was a lie. And station chief Win Scott knew it was a lie. He received reports on Oswald’s contacts with the Cubans and Russians within days. Working out of the U.S. Embassy, Charles Thomas followed up with more information about Oswald’s contacts, which were not known to the Warren Commission.

Scott kept the information to himself. More savvy than Thomas, he did not press Washington for answers. Thomas did. His persistent call for further investigation of Oswald’s Cuban contacts were forwarded to Angleton at the CIA in September 1969.

Angleton sent the State Department a note acknowledging receipt of Thomas’s information. He said he saw “no need for further action.” Not coincidentally, Thomas lost his position in the U.S. foreign service by the end of the year.

A former Navy fighter pilot who had 18 years of excellent government service, Thomas became despondent, disbelieving that his diplomatic career was over. Two years later, he committed suicide.


Trump’s Cover-Up

In a 2017 interview, Cynthia Thomas expressed hope that her husband’s tragic demise might be explained in the release of the last of the government’s JFK files

“It all seems so bizarre and complicated, like an awful spy novel from the Cold War,” Mrs. Thomas said in 2017. Her family urged President Trump to meet a legal deadline for the release of thousands more government files relating to the assassination. “My daughters and grandchildren deserve answers. I hope President Trump will give us that,” she said.

Trump disappointed Thomas and many others. In an October 2017 White House memo, the president stated that he had “no choice” (curious phrase) but to keep secret more than 15,000 JFK files until at least April 2021.

Cynthia Thomas is right. The JFK story is bizarre and complicated, often told in the cliches of bad spy novels. But the JFK fact pattern is also clear: Charles Thomas, John Whitten and Win Scott were three accomplished and experienced U.S. government officials. They did not believe the official JFK story. They sought to find the truth about the murder of the president, as they understood it. All three were thwarted by James Angleton, one of the most powerful men in the agency.

If Oswald, alone and unaided, killed JFK, what did Angleton have to fear from any of them?

‘Team of Rogues’

Rolf Mowatt-Larssen
Rolf Mowatt-Larssen, former CIA station chief

The consoling belief that JFK was killed by a “lone nut” or “a pro-Castro marksman” is losing credibility even in the ranks of the CIA.

Last year, Rolf Mowatt-Larssen, a former CIA station chief in Moscow, told a conference of intelligence professionals that his study of JFK’s assassination indicated that, if there was a conspiracy, the president was killed by enemies in the CIA’s Miami station.

According to an account on Medium by veteran Washington reporter Nina Burgleigh, “Mowatt-Larssen, using his access to classified CIA files, went looking for officers who would have had a motive, and access to information about Oswald.

“It takes an agent to find a mole,” he said. “Who would betray his country? We were looking for a team of rogues.”

Mowatt-Larssen’s prime suspect is a senior officer in agency’s failed Bay of Pigs invasion. His alleged motive: JFK’s Cuba policy.

“The rogues must be expert, and they need a motive,” Mowatt-Larssen explained. “To me, JFK is the motive. He pulled the plug on the Bay of Pigs. And he was reckless. He almost got us into a thermonuclear war with the Soviets.”

Mowatt-Larssen’s conclusions are hardly definitive but his reasoning is logical. Given his expertise, his work deserves to be checked. He is asking the right questions, the same sort of questions that cost Charles Thomas his job, his career, and his life.

Source: Cynthia Thomas, State Department widow who won presidential apology, dies at 82 – The Washington Post

COME BACK TOMORROW FOR JFK STORY #25: G. Robert Blakey, chief of the HSCA investigation, recounts how the CIA stonewalled him and the U.S. Congress.





  1. Bogman says:

    It’s interesting to me that Mowatt-Larssen, a former CIA station chief, does think it’s ‘doable’ for intelligence officers to conspire and pull off the crime of the century and get away with it.

    But if it was a rogue operation at JMWAVE, Helms and Angleton can only be considered accessories after the fact with their lies and subterfuge, and are just as culpable to my mind.

    What is also interesting is that ‘mainstream’ people seems to be getting a bit more comfortable that there’s more to the assassination story than what was put out by the govt in the early 60s.

  2. George Simmons says:

    Thank you for this excellent piece, Mr Morley.

    It appears to me that Oswald’s anti/pro Castro links certainly require thorough investigation.

    When George Joannides misled and lied to the HSCA it was an obstruction of congress, a felony.
    He told the HSCA investigators that he could not find the DRE file and that there was no case agent for the DRE. Yet, he himself was the case agent, instructing them on what to do, and handing them $51,000 a month. All this at at time when the DRE were fighting with Oswald on the streets of New Orleans and then challenging him to a radio debate. What was George Joannides trying to hide? If we can find the answer to that question, I believe we can understand the assassination much better.

    Personally, I feel that the source of any conspiracy would not be Castro himself, but rather the anti-castro operation comprising of the CIA, mafia and anti castro cubans, and that Oswald’s pro Castro activities in New Orleans may have been an intelligence operation.

    I feel that every journalist in America should be asking why Joannides misled and lied to the HSCA.

    • Bogman says:

      Or how Helms lied under oath to both the WC and HSCA about his intimate knowledge of Joannides and the DRE: ‪https://link.medium.com/4pDUVvZRpV‬

    • Warren Paaton says:

      Moreover, journalists should be seeking the true authors of the executive action and the coverup, as well as the consequences for America today.

    • Gerry Simone says:


      The “no choice” link is for the 1st postponement to April 26, 2018, not the second one until 2021. Perhaps, you can include the latter in a separate link?

      Thank you.

      • Mike says:

        Trump had “no choice” because the CIA has the goods on him. That also could be the reason we have a former CIA guy as the AG.

    • Gerry Simone says:

      “Personally, I feel that the source of any conspiracy would not be Castro himself, but rather the anti-castro operation comprising of the CIA, mafia and anti castro cubans, and that Oswald’s pro Castro activities in New Orleans may have been an intelligence operation.”

      I wholeheartedly agree George!

  3. Warren Patton says:

    Exceptional analysis. Thank you for putting the Thomas research into context, which Shenon failed to do. The issue was ultimately the deceit of the CIA in covering up a murder in which it had a vested interest.

  4. Russ Tarby says:

    These four men — Thomas, Whitten, Scott and Mowatt-Larssen — were/are intelligence insiders who knew how things worked there and also knew how to determine who pulled the strings. Their well-informed doubts speak volumes.

  5. LH says:

    It takes serious nerve to send Joannides to the HSCA. Unless you know that you are above any meaningful type of review. CIA by 1950’s was running it’s own foreign policy programs, untethered from the executive branch. Dulles worked for corporate not elected bosses. Truman predicted what CIA would become, not sure even he knew how far back the control went.

  6. Zandalf says:

    I’m not sure this answers why Charles Thomas killed himself – and not that it could. It’s certainly another mystery related to the JFK murder… Very sad for Cynthia, who sounds like she knew “things” were wrong about the JFK assassination, but, perhaps seeing what “they” did to people like Mary Meyer, or Dorothy Kilgallen, mostly played it cool… just like Oswald’s wife….

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