The good spy: how the quashing of an honest C.I.A. investigator helped launch 40 years of JFK conspiracy theories and cynicism about the Feds.

• Author: Morley, Jefferson

It was 1:30 in the morning of Nov. 23, 1963, and John F. Kennedy had been dead for 12 hours. His corpse was being dressed at Bethesda Naval Hospital, touched and retouched to conceal the ugly bullet wounds. In Dallas, the F.B.I. had Lee Harvey Oswald in custody.

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 has 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 has attempt to shoot a right-wing JFK critic, a diary of has efforts to confront anti-Castro exiles in New Orleans, and has 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 blueribbon 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 investigation 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...