For years, as the government has declassified and published documents related — some very tenuously — to the assassination of President John F. Kennedy, the assumption expressed by conspiracy theorists and some historians was that anything still being withheld could be big.
That assumption led some of President Trump’s allies, including Kennedy’s nephew, Robert F. Kennedy Jr., who is now the nation’s top health official, to push him to release the final tranche of files from the Kennedy archives, believing they might reveal damning evidence: namely, that Kennedy was not assassinated by a lone gunman in Dallas.
But with the release of nearly 64,000 pages by the National Archives over the past 24 hours, including some that previously included redactions, it is becoming clear that something else might have been behind the secrecy: protecting the sources and occasionally unsavory practices of U.S. intelligence operations.
The documents are still being reviewed, so there could still be major revelations ahead, though historians consider that highly unlikely.
But judging by one standard — reviewing previously released items that are no longer redacted — the real concern appeared to be that this tranche would provide friend and foe alike the names of still living C.I.A. agents and informants, intelligence-gathering operations directed at allies, covert operations and even C.I.A. budgets.
Case in point: files detailing how the C.I.A. was gathering clandestine information in Cuba. One example comes from a presidential intelligence memo dated Nov. 23, 1963, the day after Kennedy was killed, and presumably addressed to the new president, Lyndon B. Johnson.
A version previously made public revealed that “Cuban interpreters are now posted at several surface-to-air missile (SAM) sites on the island.” Blocked out in the public version of the document, at least until Tuesday night, were the words saying how that information was obtained: “In the past week we intercepted Cuban military messages.”
In another striking example, Arthur Schlesinger Jr., a top White House aide, reported to Kennedy on the day of his inauguration in 1961 that “47 percent of the political officers serving in United States embassies were” intelligence officers working under diplomatic cover — spies, in other words.
Schlesinger also told the new president that 123 agency personnel listed as “diplomats” were actually C.I.A. agents. (Not news to those of you who watched “Homeland.”) That information was not included in previous document releases. It was this time.
The C.I.A. has always been very secretive about its operation. That is understandable, given the nature of spycraft, but also because of its history of sometimes questionable practices. A relevant example was the Bay of Pigs invasion, a failed U.S. military landing in Cuba under Kennedy.
This could help explain the shambolic nature of the latest document reveal. Piles of uncategorized documents were dumped into the public arena in two tranches after Mr. Trump abruptly announced on Monday that the documents would be released the next day.
It all suggested a last-gasp effort by the intelligence community to limit what was being shared with the public.
“The holdup was not because of the smoking guns that would help us understand Lee Harvey Oswald’s role in the assassination,” said Timothy Naftali, an adjunct professor at Columbia University and a former director of the Nixon presidential library. “It’s because ensnared in these documents were these sources and methods.”
“We were intercepting messages from Egypt,” Professor Naftali said, citing evidence in the documents that the United States was intercepting the communications of an ally during the Kennedy years. “That has nothing to do with who killed Kennedy.”
Intelligence officials have been successful for decades in holding back such revelations. This time, they ran up against two forces.
The first was that much of this information is 60 years old. It’s hard to see how disclosures from so long ago could still be damaging. Most of the people named are dead or retired, secret codes have long ago been rewritten, and alliances have changed.
The second force was Mr. Trump, who throughout his career has trafficked in questions about the circumstances of the Kennedy assassination. From that perspective, these added details were collateral damage. (Though perhaps not entirely: They do, read a certain way, reinforce the idea of the existence of some kind of deep state, another theory that animates Mr. Trump and many of his supporters.)
There were still missing documents and some blotted passages in the files released on Tuesday, suggesting that intelligence agencies were able to keep some things in the shadows.
But we now know that the United States was intercepting confidential communications in the 1960s by a host of countries. And the nation has now acknowledged covert operations in Greece, Finland, Brazil and Cyprus during the early 1960s.
“For students of international affairs, we now have evidence of them intercepting and reading the official communications of Indonesia and Egypt during the Kennedy era,” Mr. Naftali said.
“For J.F.K. assassination buffs,” he added, “this is all a big nothingburger.”
