John McCone came to the CIA as an outsider. An industrialist and an engineer by training, he replaced veteran spymaster Allen Dulles as director of central intelligence in November 1961, after John F. Kennedy had forced out Dulles following the CIA’s bungled operation to oust Fidel Castro by invading Cuba’s Bay of Pigs. McCone had one overriding mission: restore order at the besieged CIA. Kennedy hoped his management skills might prevent a future debacle, even if the Californian—mostly a stranger to the clubby, blue-blooded world of the men like Dulles who had always run the spy agency—faced a steep learning curve. 
 
 After JFK’s assassination in Dallas in November 1963, President Lyndon Johnson kept McCone in place at the CIA, and the CIA director became an important witness before the Warren Commission, the panel Johnson created to investigate Kennedy’s murder. McCone pledged full cooperation with the commission, which was led by Chief Justice Earl Warren, and testified that the CIA had no evidence to suggest that Lee Harvey Oswald, the assassin, was part of any conspiracy, foreign or domestic. In its final report, the commission came to agree with McCone’s depiction of Oswald, a former Marine and self-proclaimed Marxist, as a delusional lone wolf. 
 
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 But did McCone come close to perjury all those decades ago? Did the onetime Washington outsider in fact hide agency secrets that might still rewrite the history of the assassination? Even the CIA is now willing to raise these questions. Half a century after JFK’s death, in a once-secret report written in 2013 by the CIA’s top in-house historian and quietly declassified last fall, the spy agency acknowledges what others were convinced of long ago: that McCone and other senior CIA officials were “complicit” in keeping “incendiary” information from the Warren Commission. 
 
 According to the report by CIA historian David Robarge, McCone, who died in 1991, was at the heart of a “benign cover-up” at the spy agency, intended to keep the commission focused on “what the Agency believed at the time was the ‘best truth’—that Lee Harvey Oswald, for as yet undetermined motives, had acted alone in killing John Kennedy.” The most important information that McCone withheld from the commission in its 1964 investigation, the report found, was the existence, for years, of CIA plots to assassinate Castro, some of which put the CIA in cahoots with the Mafia. Without this information, the commission never even knew to ask the question of whether Oswald had accomplices in Cuba or elsewhere who wanted Kennedy dead in retaliation for the Castro plots. 
 
 While raising no question about the essential findings of the Warren Commission, including that Oswald was the gunman in Dallas, the 2013 report is important because it comes close to an official CIA acknowledgement—half a century after the fact—of impropriety in the agency’s dealings with the commission. The coverup by McCone and others may have been “benign,” in the report’s words, but it was a cover-up nonetheless, denying information to the commission that might have prompted a more aggressive investigation of Oswald’s potential Cuba ties. 
 
 Initially stamped “SECRET/NOFORN,” meaning it was not to be shared outside the agency or with foreign governments, Robarge’s report was originally published as an article in the CIA’s classified internal magazine, Studies in Intelligence, in September 2013, to mark the 50th anniversary of the Kennedy assassination. The article, drawn from a still-classified 2005 biography of McCone written by Robarge, was declassified quietly last fall and is now available on the website of The George Washington University’s National Security Archive. In a statement to POLITICO, the CIA said it decided to declassify the report “to highlight misconceptions about the CIA’s connection to JFK’s assassination,” including the still-popular conspiracy theory that the spy agency was somehow behind the assassination. (Articles in the CIA magazine are routinely declassified without fanfare after internal review.) 
 
 Robarge’s article says that McCone, quickly convinced after the assassination that Oswald had acted alone and that there was no foreign conspiracy involving Cuba or the Soviet Union, directed the agency to provide only “passive, reactive and selective” assistance to the Warren Commission. This portrait of McCone suggests that he was much more hands-on in the CIA’s dealings with the commission—and in the agency’s post-assassination scrutiny of Oswald’s past—than had previously been known. The report quotes another senior CIA official, who heard McCone say that he intended to “handle the whole (commission) business myself, directly.” 
 
 The report offers no conclusion about McCone’s motivations, including why he would go to lengths to cover-up CIA activities that mostly predated his time at the agency. But it suggests that the Johnson White House might have directed McCone to hide the information. McCone “shared the administration’s interest in avoiding disclosures about covert actions that would circumstantially implicate [the] CIA in conspiracy theories and possibly lead to calls for a tough US response against the perpetrators of the assassination,” the article reads. “If the commission did not know to ask about covert operations about Cuba, he was not going to give them any suggestions about where to look.” 
 
 In an interview, David Slawson, who was the Warren Commission’s chief staff investigator in searching for evidence of a foreign conspiracy, said he was not surprised to learn that McCone had personally withheld so much information from the investigation in 1964, especially about the Castro plots. 
 
 “I always assumed McCone must have known, because I always believed that loyalty and discipline in the CIA made any large-scale operation without the consent of the director impossible,” says Slawson, now 84 and a retired University of Southern California law professor. He says he regrets that it had taken so long for the spy agency to acknowledge that McCone and others had seriously misled the commission. After half a century, Slawson says, “The world loses interest, because the assassination becomes just a matter of history to more and more people.” 
 
 The report identifies other tantalizing information that McCone did not reveal to the commission, including evidence that the CIA might somehow have been in communication with Oswald before 1963 and that the spy agency had secretly monitored Oswald’s mail after he attempted to defect to the Soviet Union in 1959. The CIA mail-opening program, which was later determined to have been blatantly illegal, had the code name HTLINGUAL. “It would be surprising if the DCI [director of central intelligence] were not told about the program” after the Kennedy assassination, the report reads. “If not, his subordinates deceived him. If he did know about HTLINGUAL reporting on Oswald, he was not being forthright with the commission—presumably to protect an operation that was highly compartmented and, if disclosed, sure to arouse much controversy.” 
 
 In the 1970s, when congressional investigations exposed the Castro plots, members of the Warren Commission and its staff expressed outrage that they had been denied the information in 1964. Had they known about the plots, they said, the commission would have been much more aggressive in trying to determine whether JFK’s murder was an act of retaliation by Castro or his supporters. Weeks before the assassination, Oswald traveled to Mexico City and met there with spies for the Cuban and Soviet governments—a trip that CIA and FBI officials have long acknowledged was never adequately investigated. (Even so, Warren Commission staffers remain convinced today that Oswald was the lone gunman in Dallas, a view shared by ballistics experts who have studied the evidence.) 
 
 In congressional testimony in 1978, after public disclosures about the Castro plots, McCone claimed that he could not have shared information about the plots with the Warren Commission in 1964 because he was ignorant of the plots at the time. Other CIA officials “withheld the information from me,” he said. “I have never been satisfied as to why they withheld the information.” But the 2013 report concluded that “McCone’s testimony was neither frank nor accurate,” since it was later determined with certainty that he had been informed about the CIA-Mafia plots nine months before his appearance before the Warren Commission. 
 
 Robarge suggests the CIA is responsible for some of the harsh criticism commonly leveled at the Warren Commission for large gaps in its investigation of the president’s murder, including its failure to identify Oswald’s motive in the assassination and to pursue evidence that might have tied Oswald to accomplices outside the United States. For decades, opinion polls have shown that most Americans reject the commission’s findings and believe Oswald did not act alone. Four of the seven commissioners were members of Congress, and they spent the rest of their political careers badgered by accusations that they had been part of a coverup. 
 
 “The decision of McCone and Agency leaders in 1964 not to disclose information about CIA’s anti-Castro schemes might have done more to undermine the credibility of the commission than anything else that happened while it was conducting its investigation,” the report reads. “In that sense—and in that sense alone—McCone may be regarded as a ‘co-conspirator’ in the JFK assassination ‘cover-up.’” 
 
 If there was, indeed, a CIA “cover-up,” a member of the Warren Commission was apparently in on it: Allen Dulles, McCone’s predecessor, who ran the CIA when the spy agency hatched the plots to kill Castro. “McCone does not appear to have any explicit, special understanding with Allen Dulles,” the 2013 report says. Still, McCone could “rest assured that his predecessor would keep a dutiful watch over Agency equities and work to keep the commission from pursuing provocative lines of investigation, such as lethal anti-Castro covert actions.” (Johnson appointed Dulles to the commission at the recommendation of then-Attorney General Robert Kennedy.) 
 
 The 2013 report also draws attention to the contacts between McCone and Robert Kennedy in the days after the assassination. In the wake of the Bay of Pigs disaster in 1961, the attorney general was asked by his brother, the president, to direct the administration’s secret war against Castro, and Robert Kennedy’s friends and family acknowledged years later that he never stopped fearing that Castro was behind his brother’s death. “McCone had frequent contact with Robert Kennedy during the painful days after the assassination,” the report says. “Their communication appears to have been verbal, informal and, evidently in McCone’s estimation, highly personal; no memoranda or transcripts exist or are known to have been made.” 
 
 “Because Robert Kennedy had overseen the Agency’s anti-Castro covert actions—including some of the assassination plans—his dealings with McCone about his brother’s murder had a special gravity,” the report continues. “Did Castro kill the president because the president had tried to kill Castro? Had the administration’s obsession with Cuba inadvertently inspired a politicized sociopath to murder John Kennedy?” 
 
 The declassification of the bulk of the 2013 McCone report might suggest a new openness by the CIA in trying to resolve the lingering mysteries about the Kennedy assassination. At the same time, there are 15 places in the public version of the report where the CIA has deleted sensitive information—sometimes individual names, sometimes whole sentences. It is an acknowledgement, it seems, that there are still secrets about the Kennedy assassination hidden in the agency’s files. 
 
 Philip Shenon, a former Washington and foreign correspondent for the New York Times, is author, most recently, of A Cruel and Shocking Act: The Secret History of the Kennedy Assassination. ||||| If President Donald Trump is true to his word, the American public is about to be flooded with thousands of long-secret documents that could help resolve at least some of the conspiracy theories about a turning point in the nation’s history— the assassination in 1963 of President John F. Kennedy. 
 
 In a message on Twitter on Wednesday afternoon, Trump announced that “the long anticipated release of the #JFKFiles will take tomorrow. So interesting!” 
 
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 The president did not specify whether the still-secret library of assassination-related documents will be released in full on Thursday, or whether he will give in to last-minute appeals from the CIA and FBI to block the declassification of some of the files. Either way, this promises to be a mammoth document dump. The library at the National Archives is said to include about 3,100 files that have never been seen before, most of them from the CIA, FBI and Justice Department, as well as the full text of more than 30,000 other files that were previously released in part. 
 
 The files, which are supposed to be released on the Archives website, are being made public under a deadline set by a 1992 law, the JFK Assassination Records Collection Act . The law, which Congress hoped would help tamp down the raging conspiracy theories revived or created by Oliver Stone’s film “JFK” the year before, was responsible for the release of millions of pages of other documents in the 1990s. What has remained secret at the Archives until this week were documents that the CIA, FBI and other agencies felt might somehow damage national security if made public. But short of Trump’s intervention, all of those documents must be made public, too—every word—to meet the 25-year deadline set by the law. That is the deadline that arrives on Thursday. 
 
 How to begin to go through that massive document dump—tens of thousands, if not hundreds of thousands, of pages? It will be daunting even for historians, researchers and others who study the assassination and have been eagerly anticipating, for decades, the chance to see the files. 
 
 For most people who are not longtime students of the assassination, there will be almost instant frustration with the files because it will be impossible to make sense of most of the documents—at least not quickly. Many will be jam-packed with CIA and FBI code names, pseudonyms and other jargon, while other documents will be in foreign languages or refer to people and places never previously connected to the assassination—probably because those people and places had nothing to do with JFK’s murder but got swept up in earlier investigations. And, based on past releases, some of the documents will be virtually impossible to read because—apparently—the ink on the paperwork had so faded by the time digital copies were made. 
 
 But if you’re reading this, chances are you’re undeterred by these obstacles and are eager to dive in to what is one of the most highly anticipated document dumps in American history. So what follows, based on years of research for my own 2013 history on the Warren Commission, is a list of 10 suggestions for armchair detectives who are planning to test their patience—and risk their eyesight and even their sanity—by digging into this digital mountain of paperwork: 
 
 1. Begin with the most secret documents. Start with the 3,100 assassination-related documents that the public has never seen before. It is tantalizing to ponder what could be in a document linked to the president’s murder that is so sensitive that not a single word of it could be made public until now. In previous Archives releases, those documents, when declassified, were labeled with the words: “Formerly Withheld in Full.” 
 
 2. Focus on Mexico City. Many historians, journalists and researchers who have studied the assassination, including this one, argue that the most important, and mostly unexplored, mysteries about the assassination involve the gunman Lee Harvey Oswald’s six-day trip to Mexico City in late September 1963, just weeks before JFK’s murder. The index released by the Archives shows that many of the soon-to-be-released documents are drawn from the files of the CIA station in Mexico City; that includes the paperwork of officers involved in the surveillance of Oswald during the Mexico trip. From what has already been made public, Oswald, a self-proclaimed Marxist who had once tried to defect to the Soviet Union, was in contact with Cuban and Soviet spies in Mexico and is reported to have talked openly there of his intention to kill Kennedy. The question has always been: How much did the CIA station in Mexico City know in real time about those contacts and a possible threat to Kennedy’s life—and was all that intelligence passed back to CIA headquarters? 
 
 3. Keep in mind that the crazy theory about an Oswald “imposter” in Mexico may not be so crazy. Oswald did indeed go to Mexico City and appeared at the Cuban and Soviet embassies—several witnesses confirmed it, and there is other evidence—but many popular conspiracy theories focus on the possibility that a CIA agent or someone else impersonated Oswald in Mexico for at least part of the trip. After the assassination, there was special confusion within the FBI and CIA over reports that telephone calls in Mexico City—on phones tapped by the CIA—suggested that a man claiming to be Oswald in calls with the Soviet and Cuban embassies was someone else; the voice sounded different. Was the caller actually working for the CIA? That seems possible, if only because the CIA’s Mexico City station had a program of trying to intercept potential Americans defectors or spies who, at the height of the Cold War, regularly showed up at the door of Cuban and Soviet embassies in Mexico. Was it possible that the CIA, learning of Oswald’s arrival in Mexico, sent an agent to intercept him before some of his planned meetings with Cuban or Soviet agents, or that a CIA agent pretended to be Oswald in some of the phone calls? The CIA officer who ran operations directed at the Cuban embassy was David Atlee Phillips, and his files are among the documents scheduled to be released this week. The CIA claimed to the Warren Commission it had no surveillance photos of Oswald in Mexico and had routinely erased tapes of his wiretapped phone calls there; CIA officers would tell Congress years later that photos and tapes had survived. 
 
 4. Credit Oliver Stone, Kevin Costner and the power of Hollywood. There is plenty of irony in the fact that it took a conspiracy-theorist filmmaker like Stone to create the uproar that led, ultimately, to the release of all of the government’s secret files about JFK. Nearly as ironic: that the final decision about releasing the files is left to Trump, who has promoted unsupported conspiracy theories throughout his adult life, including one offered during last year’s campaign that tied Senator Ted Cruz’s father to Oswald. And here's a further irony: The film's hero, the late New Orleans District Attorney Jim Garrison, played by Costner, was no hero. He was a charlatan whose allegations that a prominent New Orleans businessman was part of a CIA-directed conspiracy to kill Kennedy fell apart when the case was finally brought to a jury; Garrison’s tactics against another man in the case appear to have driven him to suicide. Among the champions of the 1992 bill: Senator Arlen Specter, the Pennsylvania Republican who first gained national fame in the 1960s as the Warren Commission staff member who developed the so-called single bullet theory—the theory that one bullet from Oswald’s rifle hit both Kennedy and Texas Governor John Connally, who was a passenger in Kennedy’s limousine. The single bullet theory, while almost certainly true, was ridiculed in the film, as was Specter, by name. 
 
 5. Don’t forget that the government has already admitted there was a JFK assassination “cover-up,” just not the one Oliver Stone imagined. In a once-classified 2013 report, the CIA’s in-house historian acknowledged that the spy agency had conducted a “cover-up” (albeit a “benign cover-up,” he said) to hide “incendiary” information from the Warren Commission that might have pointed away from Oswald as the man solely responsible for Kennedy’s murder. The CIA wanted the commission to focus solely on “what the Agency believed at the time was the ‘best truth’—that Lee Harvard Oswald, for as yet undetermined motives, had acted alone.” According to the report, the most important information withheld from the Warren Commission: The CIA had been trying, for years, to assassinate Fidel Castro. Without that information, the commission never even knew to ask whether Oswald had accomplices in Cuba, Mexico or somewhere else who wanted Kennedy dead in retaliation for the Castro plots. 
 
 6. Remember who wrote these documents. These will be, mostly, documents written by federal government workers to other government workers, using jargon that would mean little to anyone outside their agencies, even when discussing the details of a turning point in history like the Kennedy assassination. Previously declassified documents have demonstrated that embarrassing or explosive information about the assassination tended to be hidden in bureaucratic language found in the middle or at the bottom of the paperwork. An example of information buried in previously declassified files: a 1967 CIA memo that revealed tantalizing information about “the fact” of a brief affair between Oswald and a Mexican woman who worked in the Cuban consulate in Mexico City. “The fact” was characterized as insignificant and worthy of no one’s attention. 
 
 7. Bone up on your Watergate history. The long-secret assassination files cite the activities of a remarkable number of CIA officials and American political operatives who later turn up as figures in the Watergate scandals of the Nixon administration. The files include an 84-page background file on Bernard Barker, a Cuban exile who was one of the Watergate burglars, as well as documents on Watergate conspirator E. Howard Hunt, an ex-CIA officer whose family has insisted that he might have had advance knowledge of the JFK assassination. 
 
 8. Find a good cheat sheet and other shortcuts. Several websites are dedicated to questions—and conspiracy theories—about the assassination. One is especially valuable: the website of the Mary Ferrell Foundation, which has created a vast online archives of government files and other information about the assassinations of both John and Robert Kennedy, and of Martin Luther King. Last year, the foundation’s president, Rex Bradford, prepared a useful summary of the soon-to-be released documents. The website also has prepared an invaluable guide to the meaning of thousands of the CIA code names used to identify people and programs that figure in the history of the Kennedy assassination. Another valuable website for JFK assassination research: www.JFKfacts.org. The site is run by Jefferson Morley, a former journalist at the Washington Post and the author of a biography of Winston Scott, the CIA station chief in Mexico at the time of Oswald’s visit. 
 
 9. Remember the name James Jesus Angleton. Angleton was the CIA’s counterintelligence director at the time of the Kennedy assassination and controlled the flow of information to the Warren Commission. Angleton, a paranoid, delusional, duplicitous alcoholic whose legacy at the CIA is a uniquely disastrous one, appears to have intentionally withheld evidence and witnesses from the commission, all but guaranteeing its investigation would be flawed. Among the most intriguing documents scheduled for release this week is a top-secret 74-page transcript of a 1976 interview with Angleton by congressional investigators. 
 
 10. Forget the name of Rafael Cruz Sr. (probably). Cruz, the 78-year-old father of Senator Ted Cruz, is the subject of the conspiracy theory offered by Trump during last year’s campaign. President-to-be Trump repeatedly promoted an article in the National Enquirer that suggested ties between Rafael Cruz and Lee Harvey Oswald, based on a photograph from the files of the Warren Commission that showed Oswald and man who resembled Cruz Sr. in the streets of New Orleans. Both Senator Cruz and his father, who grew up in Cuba, adamantly denied any family tie to Oswald. And no other evidence has emerged to suggest any connection. 
 
 
 
 Philip Shenon, a former Washington and foreign correspondent for the New York Times, is author, most recently, of A Cruel and Shocking Act: The Secret History of the Kennedy Assassination. ||||| COLLEGE PARK, Md. — Shortly after the 1963 assassination of President John F. Kennedy, Chief Justice Earl Warren, who oversaw the first official inquiry, was asked by a reporter if the full record would be made public. 
 
 “Yes, there will come a time,” the chairman of the Warren Commission responded. “But it might not be in your lifetime.” 
 
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 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. 
 
 Clockwise from top left: E. Howard Hunt: There are at least 332 pages of material in the final collection on Hunt, who is most famous for running the ring that broke into Democratic Party headquarters in the Watergate Hotel in 1972. A decade before, 
 
 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 collection includes thousands of files that were partially released over the years but with key sections blacked out, like the CIA’s official history of its Mexico City station (which was opened in 1950 by E. Howard Hunt). Rex Bradford – who runs 
 
 “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.”
– Think the CIA played a role in covering up the John F. Kennedy assassination? Now an important source agrees with you: the CIA. According to an article written by the agency's senior in-house historian, the CIA purposely held back information from the Warren Commission, Politico reports. John McCone, then the agency's director, apparently failed to tell the commission about agency plots to murder Fidel Castro (including ones involving the Mafia). So the commission never knew to ask whether Lee Harvey Oswald had Cuban comrades dead-set on retaliating against the US president. The commission famously concluded that Oswald acted alone, spawning decades of conspiracy theories involving Castro, the Mafia, the CIA, the Soviets, and even President Lyndon B. Johnson. Seems the White House nudged McCone along: He "shared the administration’s interest in avoiding disclosures about covert actions that would circumstantially implicate [the] CIA in conspiracy theories and possibly lead to calls for a tough US response against the perpetrators of the assassination," reads the article, which was published in a CIA internal magazine in 2013 and declassified (with 15 redactions) last fall. McCone also apparently didn't reveal that the CIA may have been communicating with Oswald before the killing, and was illegally reading his mail after he tried defecting to the Soviets in 1959. The article, by CIA historian David Robarge, calls McCone's actions "benign" but says the cover-up played a big role in "undermin[ing] the credibility of the commission." (Click for a list of the most pervasive JFK conspiracy theories.)