The FBI and the CIA are still protecting their sources from six decades ago.

Almost exactly 59 years after those rifle shots rang out in Dealey Plaza, left a president mortally wounded and changed the course of history, there are still secrets that the government admits it is determined to keep about the November 1963 assassination of President John F. Kennedy. More than 14,000 classified documents somehow related to the president’s murder remain locked away, in part or in full, at the National Archives in clear violation of the spirit of a landmark 1992 transparency law that was supposed to force the release of virtually all of them years ago.

The fact that anything about the assassination is still classified — and that the CIA, FBI and other agencies have refused to provide the public with a detailed explanation of why — has convinced an army of conspiracy theorists that their cynicism has always been justified.

Newly released internal correspondence from the National Archives and Records Administration reveals that, behind the scenes, there has been a fierce bureaucratic war over the documents in recent years, pitting the Archives against the CIA, FBI and other agencies that want to keep them secret.

The correspondence, obtained under the Freedom of Information Act, shows that the Archives has tried, and often failed, to insist that other agencies comply with the 1992 law by declassifying more documents. The struggle was especially fierce in 2017, when then-President Donald Trump sided with the CIA and FBI and agreed to waive a supposedly concrete legal deadline that year to release all classified documents related to the JFK assassination.

Last year, President Joe Biden ordered another review of the documents to allow more to be made public this December. Officials involved in the declassification process say they are optimistic that a large batch of documents will be made public next month.

The internal correspondence from the Archives helps resolve one lingering mystery about the documents: In their negotiations with the White House and the Archives in recent years, how have the CIA, FBI, the Pentagon and other agencies justified keeping any secrets about a turning point in American history that occurred decades ago — an event that has always inspired corrosive conspiracy theories about government complicity?

In the past, those agencies have provided the public with only vague explanations about their reasoning, citing potential damage to national security and foreign policy.

The Archives correspondence reveals, for the first time, their detailed justifications, providing a rare window into reasoning inside the CIA and FBI. In many cases, it shows, the CIA and FBI pressed to keep documents secret because they contained the names and personal details of still-living intelligence and law-enforcement informants from the 1960’s and 1970’s who could be at risk of intimidation or even violence if they were publicly identified.

Many of those sources — now elderly, if not close to death — are foreigners living outside the United States, which means it would be more difficult for the American government to protect them from threats. The CIA has also withheld information in the documents that identifies the location of CIA stations and safehouses abroad, including several that have been in use continuously since Kennedy’s death in 1963.

The Archives correspondence shows that, while much of the still-classified information is only indirectly related to the assassination, some of it comes directly from the FBI’s “main investigative case files” about the president’s murder. That includes the all-important case files on Lee Harvey Oswald, Kennedy’s assassin, and Jack Ruby, the Dallas strip-club owner who murdered Oswald two days after Kennedy’s death.

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