The lights were still on at the Central Intelligence Agency’s headquarters in Langley, Va., John Whitten, the agency’s 43-year-old chief of covert operations for Mexico and Central America, hung up the phone with his Mexico City station chief. He had just learned something stunning: A C.I.A. surveillance team in Mexico City had photographed Oswald at the Cuban consulate in early October, an indication that the agency might be able to quickly uncover the suspect’s background.

At 1:36 am, Whitten sent a cable to Mexico City: “Send staffer with all photos of Oswald to HQ on the next available flight. Call Mr. Whitten at 652-6827.” Within 24 hours Whitten was leading the C.I.A. investigation into the assassination. After two weeks of reviewing classified cables, he had learned that Oswald’s pro-Castro political activities needed closer examination, especially his attempt to shoot a right-wing JFK critic, a diary of his efforts to confront anti-Castro exiles in New Orleans, and his public support for the pro-Castro Fair Play for Cuba Committee. For this investigatory zeal, Whitten was taken off the case.

C.I.A. Deputy Director of Plans Richard Helms blocked Whitten’s efforts, effectively ending any hope of a comprehensive agency investigation of the accused assassin, a 24-year-old ex-Marine, who had sojourned in the Soviet Union and spent time as a leftist activist in New Orleans. In particular, Oswald’s Cuba-related political life, which Whitten wished to pursue, went unexplored by the C.I.A. The blue-ribbon Warren commission appointed by President Johnson concluded in September 1964 that Oswald alone and unaided had killed Kennedy. But over the years, as information which the commission’s report had not accounted for leaked out, many would come to see the commission as a cover-up, in part because it failed to assign any motive to Oswald, in part because the government’s pre-assassination surveillance of Oswald had been more intense than the government ever cared to disclose, and finally because its reconstruction of the crime sequence was flawed.

Both the story of Oswald and the C.I.A., and the way in which it leaked out in bits and pieces fueled a generation of conspiracy-minded authors, journalists, and filmmakers who mined Richard Helms’s dubious legacy–a rich vein of ominous ambiguity and unanswered questions about one of the most jarring events of modern American history. The untimely end to Whitten’s investigation, which prevented a public airing of what the government actually knew, also contributed to a generation of public cynicism about Washington–to a national mythology of skullduggery, and the suspicion that secret agencies in Washington were up to no good and the truth never gets out. In the decades since Kennedy’s death, the “rogue C.I.A. assassin” has become a stock Hollywood character, his villainy engrained in spy movies and the popular culture.

Whitten’s story, told here for the first time, has an uncomfortable new resonance today, as the Bush administration tries to thwart investigations into, among other things, what our intelligence agencies knew about Saddam’s WMD programs before we went to war with Iraq. Whitten was a rare C.I.A. hero in the Kennedy assassination story whose personal odyssey is a poignant but unsettling reminder that inquiries into a national tragedy can be compromised early on. Intelligence mandarins, seeking to protect their positions, can override independent subordinates. Official deceptions can take decades to unravel. Embarrassing secrets, however, don’t simply go away; eventually, they filter out, as the Kennedy case shows, often doing more harm to the country than they would have had the public known the truth earlier.

John Moss Whitten was born in 1920 to an itinerant Navy family and grew up in Annapolis, Md. After graduating from the University of Maryland with straight As, he did a stint as a captain in U.S. Army intelligence during World War II, interrogating captured German officers. After the war, he studied law at the University of Virginia, and after graduating in 1947 went to work at the newly formed C.I.A. He was a confident, well-built man with sandy hair and a pompous manner. Serving in Washington and Vienna, he built a reputation as an effective, if sometimes abrasive, officer and a skilled interrogator. In March 1962, Whitten was recalled to Washington to work in the agency’s Western Hemisphere division. At his home in south Bethesda, Whitten struck neighbors as a genial State Department hand and amiable dinner-party host. At work, he was regarded as more than competent. In March 1963, he was again promoted, this time to be chief of all C.I.A. covert operations in Mexico and Central America.

Hours after the president’s assassination, Whitten found himself at the center of history. The press reported that Oswald had lived for 32 months in the Soviet Union and that an anti-Castro student group claimed he had served as a spokesman for a pro-Castro organization, the Fair Play for Cuba Committee. With a shocked nation wondering if the assassination was a communist-inspired act of war, Helms called a meeting in his office, ordered his senior staff not to discuss the assassination, and announced that Whitten would review all internal files on Oswald.

The following morning, while he was being transferred to a more secure jail in Dallas, Oswald was shot dead by nightclub owner Jack Ruby. At the same moment, Helms was delivering Whitten’s preliminary finding –that Oswald had acted alone–to President Lyndon Johnson. Whitten’s investigation continued–for the next couple of weeks, he and a staff of 30 worked almost around the clock, doggedly plowing through C.I.A. cables from all over the world, scouring for new information. He forwarded the most interesting material to the White House, under Helms’s name. He drafted a report on what the C.I.A. knew about Oswald and began circulating drafts to the various offices in the operations directorate that had tracked Oswald at one point or another. Nothing he learned in these first few weeks changed Whitten’s original assessment, that Oswald had shot President Kennedy without anyone else’s help or command.

But in the first days of December, Whitten abruptly learned that Helms had not been providing him all of the agency’s available files on Oswald. On Dec. 6, he and a colleague went to the White House to read a report the F.B.I. had been preparing on Oswald. When he finished, he walked out into the cold sunny morning, feeling stunned: The bureau, he realized, possessed information about Oswald’s past political activities that Helms had known but had never shared with him. “Oswald’s involvement with the pro-Castro movement in the United States was not at all surfaced to us [meaning him and his staff] in the first weeks of the investigation,” he later told investigators.

At a meeting soon after Dec. 6, Whitten complained to Helms and James Angleton, the chief of counter-intelligence staff, who outranked even Helms. Oswald’s involvement with pro-Castro groups, he argued, made his initial conclusions “completely irrelevant.” Analytically, Whitten had a point. Bureaucratically, he was out of line. Angleton, a pinched, brainy alcoholic who was responsible for keeping track of American defectors to the U.S.S.R. including Oswald, quickly concluded that Cuba was unimportant to the investigation, and decided to focus his inquiry narrowly on his own theories about Oswald’s life in the Soviet Union.

Whitten felt sandbagged when Helms turned the Oswald investigation over to Angleton. Helms told him his services would no longer be needed, and Whitten was sent back to his Latin America duties. His ideas for investigating Oswald’s Cuban connections were abandoned.

What Whitten didn’t know was that Helms’s reluctance to investigate Oswald’s connection to the pro-Castro movement had little to do with unraveling the Kennedy assassination–and a lot to do with hiding the potentially embarrassing performance of Helms’s top anti-Castro operatives in regards to Oswald.

In the 12 weeks prior to Nov. 22, the agency had been keeping tabs on the man who would later assassinate the president. In August, Oswald had tried to insinuate himself into the ranks of the anti-Castro Cuban Student Directorate, then turned around and started handing out pamphlets for the Fair Play for Cuba Committee. What the C.I.A. failed to disclose for more than 30 years was that the Directorate’s leaders in Miami were receiving $25,000 a month at the time. As I reported in the Miami New Times two years ago, an undercover agency officer working for Helms named George Joannides was guiding and monitoring the group’s activities at the time of its contacts with Oswald.

In September, one of the agency’s Latin American operatives had stood in line next to Oswald in New Orleans as he applied for a visa to travel to Mexico City where, two weeks later, Oswald visited the Cuban consulate. His arrival there was recorded by C.I.A. photo and audio surveillance teams reporting to a highly-regarded career officer named David Atlee Phillips, perhaps Helms’s most accomplished protg. Reports of Oswald’s presence in Mexico City went back to Langley, where they were reviewed by Helms’s top aide, Tom Karamessines. Had the agency’s investigation of Oswald proceeded the way Whitten wanted, the accused assassin’s connections to Cuba would have been fully reviewed, forcing the agency to account, at least internally, for what Joannides, Phillips, and Karamessines knew about Oswald.

Helms may have also feared that having John Whitten running loose in the C.I.A. files might expose his ongoing effort to arrange Castro’s assassination. Under Helms’s direction, C.I.A. agents had been encouraging Rolando Cubela, a charismatic young commandante who had come to power with Castro in 1959 but had later become disillusioned, to consider simply killing Castro himself. Cubela was an important asset at the heart of the Cuban government, memorably code-named AMLASH. On the day Kennedy was killed, Helms had sent an aide to bring a pen, fixed to deliver deadly poison, to Cubela in Paris. Even after Kennedy was dead, Helms continued to pursue Castro’s murder. He did not call off the AMLASH plot.

Whether Helms actually punished Whitten for attempting to pursue the Oswald investigation, we cannot tell; Whitten’s job evaluation from 1963 remains classified. But in the following years, while Helms went on to become Director of Central Intelligence, Whitten’s career stalled. In 1965, he was kicked sideways into an unimportant job reviewing operations. He would not get a senior position, but his brilliance could not be denied. In 1970, he was awarded the Distinguished Intelligence medal, the agency’s highest honor. He retired and moved his family to Vienna, where he pursued a new career as a singer.

There he found refuge in the calmer glories of Johann Strauss. Whitten became the first American to be accepted into the Vienna Men’s Choral Society, the venerable singing group whose New Year’s concerts are televised around the world. On concert nights, he sang first tenor. In his free time, he served as tour director. Gerhard Track, director of the society and a close friend of Whitten’s, told me that Whitten had wished to leave his life in America behind and never spoke about his espionage work. An honest bureaucrat, Whitten had stumbled into the middle of perhaps the greatest scandal related to one of the most momentous events in American history, but he never sought to rat on the institution which had shunted him aside. Neither a conspiracy theorist nor an apologist, he remained loyal to Langley.

The agency’s dossier on Oswald, which Whitten had tried to draw upon, would of course leak out anyway over the next two decades, tarnishing both the agency and Helms’s reputation. In 1973, President Richard Nixon, mistrusting Helms’s role in the Watergate burglary scandal, forced him out of the director’s chair. Details about Helms’s role in the assassination plots began to leak out. In May 1976, the C.I.A. connection with Rolando Cubela became public knowledge. With public outrage running high, Congress sliced the agency’s budget and reined in its activities. The Justice Department indicted Helms for misleading lawmakers about the agency’s part in overthrowing a leftist government in Chile. In 1978, Congress reopened the JFK investigation.

Whitten reluctantly returned from self-imposed exile to testify in secret session. As a former senior official who had once enjoyed access to virtually all of the agency’s files on Oswald, he greatly interested the House Select Committee on Assassinations (HSCA). On May 16, 1978, two investigators and a stenographer recorded seven hours of Whitten’s testimony about what he knew of the agency’s Oswald investigation.

At the beginning, Whitten raised his right hand and swore to tell the truth. When asked to give his name, he replied, “John Scelso,” which had been a code name he used in C.I.A. cables. But his testimony was remarkably candid. A less self-confident man might have minced his words. Not John Whitten. He sang.

Asked whether he thought Helms had acted properly by failing to disclose the Cubela plot to the Warren Commission, Whitten replied, “No. I think that was a morally highly reprehensible act, which he cannot possibly justify under his oath of office or any other standard of professional service.”

Whitten said that he believed Oswald was a “pro-Castro nut,” but he was aware of no evidence that Oswald had conspired with others. Yet he added that Helms had thwarted two important lines of inquiry: Oswald’s Cuba-related activities and the AMLASH/Cubela imbroglio. Had he known about the latter, Whitten said he would have polygraphed Cubela, which might have put to rest suspicions that the malcontent commandante could have been Castro’s double agent. Had he not been kept in the dark by Helms, Whitten said he would also have taken the investigation to the C.I.A. station in Miami, preempting decades worth of public speculation about what C.I.A. officials knew about Oswald and when they knew it.

Had Whitten been permitted to follow these leads to their logical conclusions, and had that information been included in the Warren Commission report, that report would have enjoyed more credibility with the public. Instead, Whitten’s secret testimony strengthened the HSCA’s scathing critique of the C.I.A.’s half-hearted investigation of Oswald. The HSCA concluded that Kennedy had been killed by Oswald and unidentifiable co-conspirators.

The insistence of the C.I.A. that all of the records of the HSCA investigation be kept secret for 50 years stoked more suspicion and cleared the way for Oliver Stone’s 1991 movie JFK, which portrayed the assassination as the work of high-level C.I.A. and Pentagon conspirators. The Washington press corps ripped Stone for taking liberties with the historical record. But polls show that the general public found his interpretation of Kennedy’s death more believable than the government’s. The loss of investigatory nerve that first showed in John Whitten’s reassignment culminated in permanent damage to the credibility of the U.S. government.

In 1996, Whitten’s 192-page deposition was finally declassified by the Assassination Records Review Board, an independent civilian panel created by Congress after the “JFK” furor. The board’s chairman, federal judge John Tunheim, describes the deposition as “one of the most important” new JFK records. At Whitten’s request, however, the board did not then declassify his true name. Whitten died in a Pottstown, Pa., nursing home in January 2000. Whitten’s nemesis survived him. In retirement, Richard Helms lived quietly in Washington’s Foxhall neighborhood, his number listed in the phone book. He had worked off the notoriety of the 1970s during the Reagan years when his hard-line posture became more fashionable and his legal troubles were forgotten. He was a fixture on the social circuit, attending events at the Kennedy Center and lunching with friends at the Sulgrave Club in Foggy Bottom, steadily working to rehabilitate his reputation with selected historians and journalists.

Helms never deigned to discuss “John Scelso,” the C.I.A. man who spoke so critically about him. He flicked off my requests for interviews in the late 1990s with world-weary ease. When I asked him about “John Scelso,” he said, perhaps truthfully, “I don’t think I recall the name.” Helms died at his home on Garfield Street in Washington on Oct. 22, 2002. Seven days later, the C.I.A declassified John Whitten’s name.

Jefferson Morley’s column “World Opinion Roundup” appears every Tuesday

and Thursday on washingtonpost.com. He can be reached via email at morleyj2000@yahoo.com.