The promotional material for Philip Shenon’s rollicking new book, “A Cruel and Shocking Act,” reminds us that three questions have “haunted our nation” for the past 50 years: “Was the President killed by a single gunman? Was Lee Harvey Oswald part of a conspiracy? Did the Warren Commission discover the whole truth of what happened on November 22, 1963?”

Shenon does not definitively answer the first two questions; as he acknowledges, we may never have the final word on whatever conspiracy did or did not exist. On the third matter, however, his judgment is unequivocal. The Warren Commission, he writes, was “flawed from the start” because of bureaucratic infighting, political manipulation, destruction of evidence, tight deadlines, understaffing, deception by intelligence agencies and a host of other ills. Rather than attempting to offer the Ultimate Truth of the Kennedy Assassination, Shenon presents a persuasive, deeply researched account of why, 50 years out, that truth still seems so hard to find.

He began his project with what seemed like a genuinely new angle on a familiar topic. Rather than join the legions of historians and journalists reexamining the Kennedy assassination for the 50th anniversary, he planned to focus on the Warren Commission and on the back-office wrangling that went into producing its conclusions. For Shenon, this was a natural fit. His first book, “The Commission,” dissected the 9/11 Commission, showing how political considerations and bureaucratic battles distorted its famed report. In 2008, when a former staff investigator offered to help with a “similar history” of the Warren Commission, Shenon signed on.

Something happened along the way. The final book stays true to Shenon’s original plan to write the story of the Warren Commission as told by its junior lawyers, the only members still alive to describe their experiences. Grafted onto this, though, is a spy drama involving Cuban diplomats, alluring young women and the secret love affairs of Oswald. Despite his best intentions, Shenon found himself drawn into the world of spycraft, intrigue and conspiracy that makes up both the best and the worst of the Kennedy assassination literature. The result is a book that’s one part “Mad Men” and one part James Bond.

“A Cruel and Shocking Act” takes its name from the first sentence of the Warren Commission’s report: “The assassination of John Fitzgerald Kennedy on November 22, 1963, was a cruel and shocking act of violence directed against a man, a family, a nation, and against all mankind.” And it is the commission — not the assassination — that provides the book’s basic narrative arc. The first chapter begins on the day after the president’s death, with the naval pathologist who conducted Kennedy’s autopsy burning his original notes in his home fireplace. Ostensibly, the good doctor hoped to keep the bloodstained pages out of the hands of trophy-seekers and maudlin “ghouls.” But as Shenon notes, the effect was no different than if he had been deliberately covering up a hidden truth: The notes were gone forever.

The pages that follow are filled with similarly jaw-dropping scenes involving the destruction and manipulation of evidence. Some will be familiar to Kennedy assassination devotees (here, once again, is FBI agent James Hosty crouched over a toilet in the Dallas field office, flushing a handwritten note from Oswald). Others are less well-known, such as the State Department’s apparent ostracism of diplomat Charles William Thomas for his insistence on investigating Oswald’s Cuba ties. (Thomas committed suicide in 1971.) In compiling this record, Shenon takes full advantage of the vast assassination-related material released in the past few decades, including the full run of Lyndon Johnson’s secret presidential tapes and the transcripts of the Warren Commission’s executive sessions.

The heroes of Shenon’s story are the Warren Commission’s midlevel lawyers and investigators, who in his view tried valiantly but failed to get to the bottom of the assassination mystery. As individual characters, these men can be hard to differentiate: Which one was the Yale lawyer from Ohio? Which was the Harvard man from Michigan? Shenon’s tendency toward uncritical praise of their efforts does little to help. “I am left with nothing but admiration for most of the then young staff lawyers on the commission,” he writes. It is no coincidence that these men were also his chief first-person sources, some of them opening up for the first time. Shenon’s access makes for a valuable addition to the historical record, but it does not engender much critical distance.

The book’s villains, by contrast, are the peevish old men of the intelligence establishment, including FBI Director J. Edgar Hoover and CIA counterintelligence chief James Jesus Angleton. In Shenon’s telling, these men manipulated the Warren Commission for selfish, misguided reasons, withholding information to protect their agencies from criticism and thus condemning the nation to decades of frustration and conspiracy-mongering. The FBI comes in for especially harsh treatment as a “sclerotic bureaucracy” led by a tyrannical, small-minded, rapidly aging boss.

As a generational morality tale, this makes for a compelling read. The problem is that the commission staffers never stood much of a chance. As Shenon points out, most came in with no police or investigative experience. At first, most of them did not even have the proper security clearances. Looking back, one commission staffer admitted that he “had little choice but to trust . . . his colleagues at the CIA. The commission had almost nowhere else to turn for most of the information it would need” on foreign adversaries suspected of playing a role in Kennedy’s death. In Shenon’s view, the young idealists of the Warren Commission were outmatched by an intelligence establishment with a virtual monopoly on secret information and an army of agents to gather it.

This helps to explain how the commission missed out on the evidence that makes up the second major theme of Shenon’s book: the possibility that Oswald was working for or with Cuba’s revolutionary government. As a veteran journalist and former New York Times reporter, Shenon knows to hedge his bets when it comes to conspiracy theories. All the same, he can’t help but engage the strange Cold War netherworld of Soviet defection, repatriation and pro-Castro activism in which Oswald lived during his brief adult life.

Shenon is particularly intrigued by Oswald’s September 1963 trip to Mexico City, where the future assassin tried and failed to gain Soviet and Cuban visas. While in Mexico, Shenon writes, Oswald apparently had a fling with a low-level staffer at the Cuban Consulate, and he was spotted at a Chubby Checker “twist party” attended by a Cuban diplomat deeply hostile to Kennedy. Two months later, back on American soil, Oswald shot and killed the president.

Shenon goes to great lengths to emphasize his new evidence about Oswald’s Mexico trip, and understandably so. When it comes to the most-studied murder of all time, it is no mean feat to turn up even the smallest tidbit. Still, the book stops short of suggesting a Cuban conspiracy, arguing simply that the Warren Commission (along with the FBI and the CIA) should have done more to investigate the available evidence. In the end, “A Cruel and Shocking Act” offers many of the trappings of conspiracy literature — doctored evidence, a mysterious suicide, a secret affair — without quite arguing in favor of a conspiracy.

What the book does show is something at once more sweeping and more banal: To the degree that the Warren Commission overlooked evidence or avoided subjects, the reasons were largely political and bureaucratic. The Kennedy family sought a limited autopsy, for instance, not because they feared the ballistics evidence but because they hoped to avoid exposing Kennedy’s health problems, including Addison’s disease. Similarly, CIA officials held back records on Oswald’s visit to Mexico City not because they intended to cover up a Cuban conspiracy but because they wanted to avoid revealing other wiretapping and surveillance operations. Perhaps most important, Lyndon Johnson and Earl Warren sought to limit the commission’s scope and timeline to get the whole affair out of the way before the next presidential election.

As Shenon points out, the commission’s flawed final report has ended up fueling rather than suppressing public suspicions of a high-level conspiracy — precisely the opposite of what Johnson and Warren intended. And yet one can’t help but feel sympathy for the political leaders charged with managing the assassination crisis. In the “jittery, even apocalyptic” atmosphere of 1963, Shenon writes, it seemed entirely possible that an accusation of Soviet or Cuban involvement could spark a full-blown foreign-policy crisis or even a nuclear war. In that context, the effort to limit the commission’s work may have turned out to be good politics but poor investigative history.

The price is that we may never know exactly what happened on Nov. 22, 1963. Fifty years out, we have hundreds of thousands of pages dedicated to undoing and redoing the work of the Warren Commission. But the more we find out, Shenon suggests, the more we realize how little we know. “In many ways,” he concludes, “this book is an account of my discovery of how much of the truth about the Kennedy assassination has still not been told.”

Beverly Gage is a professor of history at Yale University. She is writing a biography of J. Edgar Hoover.

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The Secret History of

the Kennedy Assassination

By Philip Shenon

Henry Holt. 625 pp. $32