“Yes, there will come a time,” the chairman of the Warren Commission responded. “But it might not be in your lifetime.”

It will soon be in ours — that is, unless the CIA, FBI or other agencies still holding on to thousands of secret documents from related probes convince the next occupant of the White House otherwise.

A special team of seven archivists and technicians with top-secret security clearances has been set up at the National Archives and Records Administration to process all or portions of 40,000 documents that constitute the final collection of known federal records that might shed light on the events surrounding JFK’s murder, POLITICO has learned — files that, according to law, must be made public by October 2017.

But the records’ release is not guaranteed, says Martha Murphy, head of the National Archives’ Special Access Branch. While the JFK Records Act of 1992 mandated the files be made public in 25 years, government agencies that created the paper trail can still appeal directly to the president to keep them hidden. And some scholars and researcher not to mention the army of JFK conspiracy theorists, fear that is exactly what will happen given the details about the deepest, darkest corners of American spy craft that could be revealed — from the inner workings of the CIA’s foreign assassination program and front companies to the role of a CIA psychological operations guru accused of misleading congressional investigators about alleged assassin Lee Harvey Oswald’s activities.

“We have sent letters to agencies letting them know we have records here that were withheld, 2017 is coming,” Murphy said in a recent interview at the primary government records repository in the D.C. suburbs. She said while no agency has formally requested a waiver yet, some “have gotten back to ask for clarification” and are seeking “more information.”

“Within our power, the National Archives is going to do everything we can to make these records open and available to the public,” she added. “And that is my only goal. There are limits to my powers, and the president of the United States has the right to say something needs to be held for longer.”

The review now underway marks the start of a long-awaited — and many would say tortuous — process to unlock more pieces of the puzzle surrounding the assassination of the nation’s 35th president. Among the questions still hotly disputed: Did Oswald, who had defected to Russia in 1959 and was tied to radical groups seeking to overthrow the communist government in Cuba, act alone — as the Warren Commission concluded? Did some U.S. officials or intelligence assets have prior knowledge of the plot? Did American leaders willfully prevent a full investigation to protect other closely guarded secrets?

At minimum, in the estimation of Murphy, who has reviewed some of the still-secret documents, they will provide a “beautiful snapshot of Cold War America and the intelligence community.” Some predict there could still be a “smoking gun.”

The documents were originally requested from dozens of agencies at the request of the Assassination Records Review Board, an independent panel of experts established by the broadly defined 1992 law that sought to collect all government records that might have a bearing on one of the most searing and vexing events of the 20th century. In all, the collection amounted to 5 million records, the vast majority of which have been made available to researchers.

But among the 40,000 documents are roughly 3,600 that have never been seen by the public. They have been “withheld in full” primarily because they contain information that was considered “security classified” but also to protect personal privacy, tax and grand jury information, and “because information in the document reveals the identity of an unclassified confidential source,” according to Murphy.

Among the 3,600 are roughly 1,100 CIA documents, which make up the largest share. The second-largest batch belongs to the FBI, according to Murphy, while the rest include testimony and other records of the Warren Commission itself; the House Select Committee on Assassinations, which reopened the investigation into JFK’s death in the late 1970s and concluded it was the result of a conspiracy (though the panel couldn’t prove it); records from the National Security Agency and other Defense Department offices; and files from a pair of 1975 congressional probes of CIA abuses — the so-called Church and Pike committees — and a related commission led by then-Vice President Nelson Rockefeller.

The withheld CIA files include those on some of the most mysterious and controversial figures in the history of American espionage — particularly individuals who were known to be involved in CIA assassination plots around the world.

There are at least 332 pages of material on E. Howard Hunt, an almost mythical spymaster who is most famous for running the ring that broke into Democratic Party headquarters in Washington’s Watergate Office Complex in 1972, setting in motion the events that led to the resignation of President Richard Nixon.

But a decade before, he played a leading role in the agency’s botched Bay of Pigs invasion in Cuba. The failed attack by CIA-trained guerrillas generated deep discontent with Kennedy from Cuban exiles seeking to overthrow Cuban leader Fidel Castro and who felt the president had let their forces die on Cuba’s beaches by refusing to provide air support against Castro’s army.

It was Hunt, shortly before he died in 2007, who claimed that he had been privy to a plot by several CIA affiliates to kill Kennedy — what he referred to as “the Big Event.”

Also under review by the special team of archivists are at least 606 pages about David Atlee Phillips, another CIA officer, who won a medal for his role in overthrowing the government of Guatemala in 1954, went on to run operations in Latin America, and, along with Hunt, played a leading role in anti-Castro activities in Cuba.

Phillips was accused — though never charged — of committing perjury when asked about agency ties to Oswald by the House Select Committee on Assassinations. Phillips, too, late in life attributed the JFK assassination to “rogue” CIA officers.

It is the type of information that many researchers believe the agency would still like to keep secret.

“I don’t see the CIA handing out 600 pages on David Atlee Phillips in two years,” said Jefferson Morley, a leading Kennedy researcher and founder of JFKfacts.org, who has sued the CIA to reveal more information about several key figures known to be the focus of some of the withheld files.

“It may have nothing to do with JFK but about other assassinations,” he added. “They still don’t want to open that window and let everyone look in. I expect the worst.”

Another colleague of Phillips at the CIA was Anne Goodpasture. The career agency officer denied to congressional investigators in 1970 that she had any knowledge of recordings of Oswald’s phone calls in possession of the CIA’s Mexico City station, where she worked. But she later admitted in sworn testimony that she had, in fact, disseminated the tapes herself. A 286-page CIA file about her is among the documents that are supposed to be released in two years.

Also among the agency’s withheld files: 2,224 pages of the CIA’s interrogation of Yuri Nosenko, a Soviet KGB officer who defected to the U.S. shortly after the Kennedy assassination. He claimed to have seen the KGB files on Oswald in the 2 ½ years before the assassination when Oswald lived in the Soviet Union.

Rex Bradford, who runs the Mary Ferrell Foundation, a research organization that has digitized more than 1 million records related to the JFK case, has also identified numerous depositions before the Church Committee that are referenced in the panel’s final report but have yet to be made public.

They include testimony on secret plots to assassinate Castro from CIA officers; Kennedy’s national security adviser, McGeorge Bundy; and the head of the CIA at the time, John McCone.

“The principal question we were trying to pursue was who ordered the assassination of Castro and five other leaders around the world — was it the president or the attorney general?” former Sen. Gary Hart, who was a member of the Church Committee and tasked with looking into the issue, said in an interview.

It was Hart’s digging that first revealed that the CIA had enlisted leading figures in organized crime to help kill Castro, who had closed down all their gambling and prostitution rings in Havana when he took power in 1959. The CIA’s assassination plots at the time have been considered by many government investigators to be relevant to finding out who might have had a motive to kill the American leader.

“How could the U.S. government bring itself to order these [CIA] assassinations?” added Hart. “We never resolved that. If these documents answer any of those questions it would be worthwhile.”

Also withheld are the Church Committee’s interviews with CIA officials about “JM/WAVE,” the code name for the secret CIA station overseeing covert operations in Cuba that was located on the campus of the University of Miami — and files on the obscure figure who ran its psychological operations branch, George Joannides.

It was revealed in a previous document release in 2009 that Joannides had links to some of the same anti-Castro forces that were connected to Oswald — something that was never shared with the Warren Commission.

Meanwhile, Joannides also served as the liaison between the agency and the House assassinations panel that reopened JFK’s murder in 1978 and inquired about the agency’s links to Oswald. But Joannides never told the panel about his role in Miami, a failure that the federal judge who ran the Assassination Records Review Board recently said amounted to “treachery.”

The CIA acknowledged in a lawsuit filed by Morley that there are more than 50 documents about Joannides’ activities, including in 1963 and 1978.

The bulk of the JFK collection now being processed by the National Archives includes thousands of files that were partially released over the years but with key sections blacked out — some of them “heavily redacted,” according to Murphy. Among these files are the CIA’s official history of its Mexico City station (which was opened in 1950 by Hunt).

Oswald visited Mexico City in the weeks before the assassination seeking visas to travel to Cuba and the Soviet Union, which he was denied. Previous government disclosures have revealed that while initially the CIA denied any knowledge of Oswald’s activities, at the time itwas monitoring him closely and created several cover stories to hide what it knew.

Meanwhile, as PBS reported in 2013, “intelligence documents released in 1999 establish that, after Oswald failed to get the visas, CIA intercepts showed that someone impersonated Oswald in phone calls made to the Soviet Embassy and the Cuban consulate and linked Oswald to a known KGB assassin — Valery Kostikov — whom the CIA and FBI had been following for over a year.”

Bradford believes the heavily redacted CIA history of the Mexico City station could still reveal new things after all these years.

“It looks very clear [from the partially released file] that they have microphones in the Cuban Embassy [in Mexico City],” he said in an interview. “When were those microphones planted? Were they operational in October [of 1963]? There is also information about human informants and spies that were inside the embassy.”

There could be more to learn from “knowing who those people were — probably dead by now, maybe not — [and] whether they see Oswald. There is all kinds of stuff in that thing that is relevant to the Oswald visit and what happened there that we only have a small glimpse into because of all the secrecy surrounding the records related to it.”

A spokesman for the CIA, Dean Boyd, said the agency is working with the National Archives on the JFK records but declined to comment on the circumstances in which the CIA might seek a waiver from the president to continue to withhold information.

“We are aware of the process and will work judiciously within that process,” he said.

Others who have closely followed the paper trail also wonder whether the additional files will shed light on how the federal government seemingly went to great lengths to obstruct the investigation into the JFK assassination (and Oswald’s killing while in police custody a few days later by Jack Ruby, the nightclub owner with Mafia ties).

Adam Walinsky, who worked in the Kennedy Justice Department, believes that the mounting evidence over the years of a purposely botched autopsy of the president and the multiple “suicides” of so many figures connected to the events strongly suggests such a coverup from high levels.

Walinsky suspects that the documents could reveal more about “the role of the FBI, under the direction of President [Lyndon] Johnson and Director [J. Edgar] Hoover, in preventing any serious investigation of the assassination at the time.”

“That is still capable of being considered a smoking gun,” he added.

But there are concerns among long-time observers of the declassification process that the battle inside the national security bureaucracy over the fate of the records is only just beginning.

“There are going to be appeals to the president, the Central Intelligence Agency for sure,” predicted Malcolm Blunt, a British researcher who has spent nearly two decades poring over JFK records. “Particularly on cover issues — corporations and financial institutions, banks and business used for cover purposes.”

David Marwell, who served as executive director of the Assassination Records Review Board from 1994 to 1997, said of the withheld records: “Often it was the stuff unrelated to the assassination but intimately related to how intelligence agencies do their business. There were practical and institutional reasons it was important for them to keep that stuff. They were very protective of relationships they had with foreign intelligence sources or situations where they might have a base or a station in a particular country.”

He also said that some of juiciest stuff about the assassination may have been destroyed or never sent to the Assassination Records Review Board in the first place.

“Unless you can enter yourself into the agencies’ files at any time and search for anything you want, how can you know you found everything?” he asked.

But Murphy, whose role is to get the 40,000 documents released, isn’t prepared to say that they won’t reveal new things about the assassination itself.

“I’ll be honest,” she says. “I am hesitant to say you’re not going to find out anything about the assassination.”

She clearly wants the secretive agencies now being consulted to decide what they want to do.

“We want this to go as smoothly as possible,” she said. “We don’t want them to wait until the last minute. It is our interest to know the status of the records as soon as possible because we are going to begin scanning them.”