"I have no choice," Trump said in a memo, citing "potentially irreversible harm" to national security if he were to allow all records to come out now. He placed those files under a six-month review while letting 2,800 others come out, racing a deadline to honor a law mandating their release.
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CLICK HERE to read the files released on the Kennedy Assassination
The documents approved for release show federal agents madly chasing after tips, however thin, in the days after the Nov. 22, 1963, assassination and juggling rumors and leads worldwide. The materials also cast a wide net over varied activities of the Kennedy administration, such as its covert efforts to upend Fidel Castro's government in Cuba.
In a Sept. 14, 1962, meeting disclosed in the files, for example, a group of Kennedy's senior aides, including brother Robert, the attorney general, discussed a range of options against Castro's communist government.
The meeting was told the CIA would look into the possibility of sabotaging airplane parts that were to be shipped to Cuba from Canada. McGeorge Bundy, JFK's national security adviser, cautioned that sensitive ideas like sabotage would have to be considered in more detail on a case-by-case basis.
As for the unreleased documents, officials say Trump will impress upon federal agencies that "only in the rarest cases" should JFK files stay secret after the six-month review.
Despite having months to prepare for disclosures that have been set on the calendar for 25 years, Trump's decision came down to a last-minute debate with intelligence agencies - a tussle the president then prolonged by calling for still more review.
In the meantime, experts will be poring through a mountain of minutiae in search of significant revelations.
Much of Thursday passed with nothing from the White House or National Archives except silence, leaving unclear how the government would comply with a law requiring the records to come out by the end of the day - unless Trump was persuaded by intelligence agencies to hold some back.
White House officials said the FBI and CIA made the most requests within the government to withhold some information.
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No blockbusters had been expected in the last trove of secret files regarding Kennedy's assassination, given a statement months ago by the Archives that it assumed the records, then under preparation, would be "tangential" to what's known about the shooting.
But for historians, it's a chance to answer lingering questions, put some unfounded conspiracy theories to rest, perhaps give life to other theories - or none of that, if the material should add little to the record.
Researchers were frustrated by the uncertainty that surrounded the release for much of the day.
"The government has had 25 years_with a known end-date_to prepare #JFKfiles for release," University of Virginia historian Larry Sabato tweeted in the afternoon. "Deadline is here. Chaos."
Trump ordered agencies that have proposed withholding material related to the assassination to report to the archivist by next March 12 on which specific information meets the standard for continued secrecy.
That standard includes details that could cause "harm to the military defense, intelligence operations, law enforcement or conduct of foreign relations," Trump wrote in his order. The archivist will have two weeks to tell Trump whether those recommendations validate keeping the withheld information a secret after April 26.
Publication of this latest trove of evidence could help allay some suspicions of conspiracy - but not for all.
"As long as the government is withholding documents like these, it's going to fuel suspicion that there is a smoking gun out there about the Kennedy assassination," said Patrick Maney, a presidential historian at Boston College.
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The full record will still be kept from the public for at least six months - and longer if agencies make a persuasive enough case for continued secrecy.
The collection includes more than 3,100 records - comprising hundreds of thousands of pages - that have never been seen by the public. About 30,000 documents were released previously - with redactions.
Whatever details are released, they're not expected to give a definitive answer to a question that still lingers for some: Whether anyone other than Lee Harvey Oswald was involved in the assassination.
The Warren Commission in 1964 concluded that Oswald had been the lone gunman, and another congressional probe in 1979 found no evidence to support the theory that the CIA had been involved. But other interpretations, some more creative than others, have persisted.
The 1992 law mandating release of the JFK documents states that all the files "shall be publicly disclosed in full" within 25 years - that meant by Thursday - unless the president certified that "continued postponement is made necessary by an identifiable harm to the military defense; intelligence operations, law enforcement, or conduct of foreign relations."
That doesn't allow the president, for example, to hold some records back because they might be embarrassing to agencies or people.
"In any release of this size, there always are embarrassing details," said Douglas Brinkley, a professor at Rice University.
The law does not specify penalties for noncompliance, saying only that House and Senate committees are responsible for oversight of the collection.