The Senate report on the intelligence failures leading to the Iraq catastrophe has not fared as well, undoubtedly because it lacked the same public oversight. This report went to even greater extremes to keep Bush out of the cross hairs. As Thomas Powers wrote in the New York Review of Books, “No tyrannical father presiding over an intimidated household was ever tiptoed around with greater caution than is the figure of President George W. Bush in the [committee's] fat report.”

And the Schlesinger report on Abu Ghraib has quickly earned itself an utterly contemptuous response, eliciting widespread outrage for giving Defense Secetary Rumsfeld and the Pentagon a sweeping pass on the reign of torture at the prison. While the world shuddered in horror at photographs and descriptions of the Abu Ghraib mayhem, James Schlesinger, the former defense secretary picked by Rumsfeld to chair the civilian commission, was considerably less agitated in his response. “Animal house,” he blithely called the prison’s chambers of violent perversity, a casual assessment that mirrored the forgiving views of Rush Limbaugh, who dismissed the scandal as a frat party gone wild.

So it is only appropriate, in this stormy season of the official version and its discontents, that we observe the 40th anniversary of the Warren Report — the mother of all such controversies. The vast, 26-volume report was delivered by the commission chairman, Chief Justice Earl Warren, to President Johnson on Sept. 24, 1964. The Warren Report concluded that President Kennedy was the victim of a lone, unstable assassin, Lee Harvey Oswald, who was himself, conveniently, gunned down just two days later in the Dallas police station by mob-connected hustler Jack Ruby. The Warren Commission — itself the victim of massive fraud and manipulation by the FBI and CIA — came under immediate fire from critics, with its report being denounced as a government coverup by a growing army of independent researchers. History has not been any kinder to the Warren Report, which has been derided and condemned by everyone from the House Select Committee on Assassinations — the only other federal panel to exhaustively probe Kennedy’s murder, and which found in 1979 that the president was the probable target of a conspiracy — to Oliver Stone in his explosive 1991 film “JFK” to the History Channel, which routinely airs even the outer limits of conspiracy theories.

Four decades later, the Warren Report is widely regarded as a whitewash, with polls consistently showing that a majority of Americans reject the official version of Kennedy’s death. (The Assassination Archives and Research Center will hold a conference to discuss the latest scholarship on the crime in Dallas and the Warren investigation from Sept. 17-19 in Washington. Information is available on its Web site.

But there is one sanctuary where the Warren Report is still stubbornly upheld and where its manifold critics can expect their own rough treatment: in the towers of the media elite. Fresh from assaulting Oliver Stone, not only for his film but for his very character (a media shark attack in which, I must confess, I too once engaged), the national press rushed to embrace Gerald Posner’s bold 1993 defense of the Warren Report, “Case Closed,” making it a bestseller. (“The most convincing explanation of the assassination,” historian Robert Dallek called it in the Boston Globe.) And the 40th anniversary of JFK’s murder last November sparked a new fusillade of anti-conspiracy sound and fury, with ABC’s Peter Jennings making yet another network news attempt to silence the report’s critics. Most of the press lords and pundits in the 1960s who allowed themselves to be convinced that the Warren Report was the correct version of what happened in Dallas — whether because they genuinely believed it or because they thought it was for the good of the country — are now dead or retired. But after buying the official version for so long, it seems the elite media institutions have too much invested in the Warren Report to change their minds now, even if they’re under new editorial leadership.

One of the great ironies of history is that while the media elite was busily trying to shore up public confidence in the Warren Report, the political elites were privately confiding among themselves that the report was a travesty, a fairy tale for mass consumption. Presidents, White House aides, intelligence officials, senators, congressmen, even foreign leaders — they all muttered darkly among themselves that Kennedy was killed by a conspiracy, a plot that a number of them suspected had roots in the U.S. government itself. (In truth, some high media dignitaries have also quietly shared their doubts about the official version. In 1993, CBS anchorman Dan Rather, who did much along with his network to enforce the party line on Dallas, confessed to Robert Tannenbaum, the former deputy chief counsel of the House Select Committee on Assassinations, “We really blew it on the Kennedy assassination.”)

Thanks to tapes of White House conversations that have been released to the public in recent years, we now know that the man who appointed the Warren Commission — President Lyndon Johnson — did not believe its conclusions. On Sept. 18, 1964, the last day the panel met, commission member Sen. Richard Russell phoned Johnson, his old political protégé, to tell him he did not believe the single-bullet theory, the key to the commission’s finding that Oswald acted alone. “I don’t either,” Johnson told him.

Johnson’s theories about what really happened in Dallas shifted over the years. Soon after the assassination, Johnson was led to believe by the CIA that Kennedy might have been the victim of a Soviet conspiracy. Later his suspicions focused on Castro; during his long-running feud with Robert Kennedy, LBJ leaked a story to Washington columnist Drew Pearson suggesting the Kennedy brothers themselves were responsible for JFK’s death by triggering a violent reaction from the Cuban leader with their “goddamned Murder Inc.” plots to kill him.

In 1967, according to a report in the Washington Post, Johnson’s suspicious gaze came to rest on the CIA. The newspaper quoted White House aide Marvin Watson as saying that Johnson was “now convinced” Kennedy was the victim of a plot and “that the CIA had something to do with this plot.” Max Holland, who has just published a study of LBJ’s views on Dallas, “The Kennedy Assassination Tapes,” intriguingly concludes that Johnson remained haunted by the murder throughout his tenure in the White House. “It is virtually an article of faith among historians that the war in Vietnam was the overwhelming reason the president left office in 1969, a worn, bitter, and disillusioned man,” writes Holland. “Yet the assassination-related tapes paint a more nuanced portrait, one in which Johnson’s view of the assassination weighed as heavily on him as did the war.”

Critics of the Warren Report’s lone-assassin conclusion were often stumped by defenders of the report with the question, “If there was a conspiracy, why didn’t President Kennedy’s own brother — the attorney general of the United States, Robert Kennedy — do anything about it?” It’s true that, at least until shortly before his assassination in June 1968, Bobby Kennedy publicly supported the Warren Report. On March 25, during a presidential campaign rally at San Fernando Valley State College in California, Kennedy was dramatically confronted by a woman heckler, who called out, “We want to know who killed President Kennedy!” Kennedy responded by saying, “I stand by the Warren Commission Report.” But at a later campaign appearance, days before his assassination, Bobby Kennedy said the opposite, according to his former press spokesman Frank Mankiewicz. When asked if he would reopen the investigation into his brother’s death, he uttered a simple, one-word answer: “Yes.” Mankiewicz recalls today, “I remember that I was stunned by the answer. It was either like he was suddenly blurting out the truth, or it was a way to shut down the questioning — you know, ‘Yes, now let’s move on.’”

His public statements on the Warren Report were obviously freighted with political and emotional — and perhaps even security — concerns for Bobby Kennedy. But we have no doubt what his private opinion of the report was — as his biographer Evan Thomas wrote, Kennedy “regarded the Warren Commission as a public relations exercise to reassure the public.” According to a variety of reports, Kennedy suspected a plot as soon as he heard his brother had been shot in Dallas. And as he made calls and inquiries in the hours and days after the assassination, he came to an ominous conclusion: JFK was the victim of a domestic political conspiracy.

In a remarkable passage in “One Hell of a Gamble,” a widely praised 1997 history of the Cuban missile crisis based on declassified Soviet and U.S. government documents, historians Aleksandr Fursenko and Timothy Naftali wrote that on Nov. 29, one week after the assassination, Bobby Kennedy dispatched a close family friend named William Walton to Moscow with a remarkable message for Georgi Bolshakov, the KGB agent he had come to trust during the nerve-wracking back-channel discussions sparked by the missile crisis. According to the historians, Walton told Bolshakov that Bobby and Jacqueline Kennedy believed “there was a large political conspiracy behind Oswald’s rifle” and “that Dallas was the ideal location for such a crime.” The Kennedys also sought to reassure the Soviets that despite Oswald’s apparent connections to the communist world, they believed President Kennedy had been killed by American enemies. This is a stunning account — with the fallen president’s brother and widow communicating their chilling suspicions to the preeminent world rival of the U.S. — and it has not received nearly the public attention it deserves.

Both Khrushchev, who had been working with JFK to ease tensions between the superpowers, and his spy chief shared Kennedy’s dark view of the assassination. KGB chairman reacted incredulously to the news that Oswald, a man whom his agency had closely monitored after he defected to the Soviet Union, was the culprit: “I thought that this man could not possibly be the mastermind of the crime.” And according to Fursenko and Naftali, “Intelligence coming to Khrushchev in the weeks following the assassination seemed to confirm the theory that a right-wing conspiracy had killed Kennedy.” This assessment was shared by the governments of Cuba, Mexico and France, where President DeGaulle, when briefed by a reporter on the lone-nut theory reacted with Gallic skepticism, laughing, “Vous me blaguez! [You're kidding me.] Cowboys and Indians!”

In the years after his brother’s death, Bobby Kennedy was overwhelmed by grief. But the common perception that he found it too painful to focus on the assassination is belied by the fact that Kennedy maintained a searching curiosity about critics of the Warren Report, using surrogates like Mankiewicz, Walter Sheridan, Ed Guthman and John Siegenthaler to check out their work and dispatching his former aides to New Orleans to evaluate Jim Garrison’s investigation. In fact Kennedy himself phoned New Orleans coroner Nicholas Chetta at his home after the death of key Garrison suspect David Ferrie to question Chetta about his autopsy report. And while Sheridan — a trusted friend of Kennedy’s who had worked closely with him on his Jimmy Hoffa investigation — famously repudiated Garrison in a 1967 documentary for NBC, RFK apparently still kept ties to the Garrison camp. According to William Turner, a former FBI agent who worked as a Garrison investigator during the Kennedy case, in April 1968 he received a call in the New Orleans prosecutor’s office from an RFK campaign aide named Richard Lubic. “He said, ‘Bill, Bobby’s going to go — he’s going to reopen the investigation after he wins.’ I went in immediately and told Jim [Garrison]. He didn’t seem surprised.”

Bobby was not the only member of President Kennedy’s inner circle who believed there was a conspiracy. Presidential aides Kenny O’Donnell and Dave Powers, key members of JFK’s Irish Mafia, were in a trailing limousine in the Dallas motorcade. Both of them later told House Speaker Tip O’Neill that they heard two shots from behind the fence on the grassy knoll. “That’s not what you told the Warren Commission,” a stunned O’Neill replied, according to his 1989 memoir, “Man of the House. “You’re right,” O’Donnell said. “I told the FBI what I had heard, but they said it couldn’t have happened that way and that I must have been imagining things.” So not wanting to “stir up more pain and trouble for the family,” O’Donnell told the commission what the FBI wanted him to.

Speaking of the FBI, its deeply sinister strongman J. Edgar Hoover might have “lied his eyes out” to the Warren Commission, as panel member Hale Boggs, the Louisiana congressman, memorably told an aide, pressuring and maneuvering the commission to reach a lone-assassin verdict. But again, in private, Hoover told another story. The summer after the assassination, Hoover was relaxing at the Del Charro resort in California, which was owned by his friend, right-wing Texas oil tycoon Clint Murchison. Another Texas oil crony of Hoover’s, Billy Byars Sr. — the only man Hoover had called on the afternoon of Nov. 22, 1963, besides Robert Kennedy and the head of the Secret Service — also was there. At one point, according to Anthony Summers, the invaluable prober of the dark side of American power, Byars’ teenage son, Billy Jr., got up his nerve to ask Hoover the question, “Do you think Lee Harvey Oswald did it?” According to Byars, Hoover “stopped and looked at me for quite a long time. Then he said, ‘If I told you what I really know, it would be very dangerous to this country. Our whole political system could be disrupted.’”

Blunt skepticism about the Warren Report was a bipartisan affair, with leaders on both sides of the aisle airily dismissing its conclusions. On a White House tape recording, President Nixon is heard telling aides that the Warren Report “was the greatest hoax that has ever been perpetuated.” One of Nixon’s top aides, White House chief of staff H.R. “Bob” Haldeman, shared his boss’ skepticism. In his 1978 memoir, “The Ends of Power,” Haldeman, who “had always been intrigued with the conflicting theories of the assassination,” recalls that when the Nixon team moved into the White House in 1969, he felt that they finally “would be in a position to get all the facts.” But Nixon, perhaps wary of where all those facts would lead, rejected Haldeman’s suggestion.

According to Haldeman, Nixon did play the assassination card in a mysterious way against CIA director Richard Helms, long regarded by Warren Report critics to have some connection to the gunshots in Dallas. Seeking to pressure the CIA into helping him out of his Watergate mess, Nixon had Haldeman deliver this cryptic message — apparently a threat — to Helms: “The president asked me to tell you this entire (Watergate) affair may be connected to the Bay of Pigs, and if it opens up, the Bay of Pigs may be blown.” This prompted an explosive reaction from the spymaster: “Turmoil in the room, Helms gripping the arms of his chair leaning forward and shouting, ‘The Bay of Pigs had nothing to do with this. I have no concern about the Bay of Pigs.’” Haldeman speculates that “Bay of Pigs” must have been Nixon’s code for something related to the CIA, Castro and the Kennedy assassination. But whatever dark card Nixon had played, it worked. Haldeman reported back to his boss that the CIA director was now “very happy to be helpful.”

Nixon was not willing to publicly reopen the box of assassination demons. But many of them began flying out when the Church Committee started investigating CIA abuses in the 1970s, including the unholy pact between the agency and the Mafia to eliminate Fidel Castro. (The bombshell headlines produced by the Church Committee would, in fact, lead to the formation of the House Select Committee on Assassinations in 1977.)

Among those in Washington who were particularly curious about the revelations concerning the CIA and the Kennedy assassination was George H.W. Bush. As Kitty Kelley observes in her new book about the Bush family, while serving as the CIA director in the Ford administration, Bush fired off a series of memos in fall 1976, asking subordinates various questions about Oswald, Ruby, Helms and other figures tied to the assassination. “Years later, when [Bush] became president of the United States, he would deny making any attempt to review the agency files on the JFK assassination,” writes Kelley in “The Family: The Real Story of the Bush Dynasty.” “When he made this claim, he did not realize that the agency would release 18 documents (under the Freedom of Information Act) that showed he had indeed, as CIA director, requested information — not once, but several times — on a wide range of questions surrounding the Kennedy assassination.”

One of the most aggressive investigators on the Church Committee was the young, ambitious Democratic senator from Colorado, Gary Hart, who along with Republican colleague Richard Schweiker began digging into the swampy murk of southern Florida in the early 1960s. Here was the steamy nursery for plots that drew together CIA saboteurs, Mafia cutthroats, anti-communist Cuban fanatics and the whole array of patriotic zealots who were determined to overthrow the government of Cuba — the Iraq of its day. “The whole atmosphere at that time was so yeasty,” says Hart today. “I don’t think anybody, Helms or anybody, had control of the thing. There were people clandestinely meeting people, the Mafia connections, the friendships between the Mafia and CIA agents, and this crazy Cuban exile community. There were more and more layers, and it was honeycombed with bizarre people. I don’t think anybody knew everything that was going on. And I think the Kennedys were kind of racing to keep up with it all.”

Schweiker’s mind was blown by what he and Hart were digging up — there is no other way to describe it. He was a moderate Republican from Pennsylvania and he would be chosen as a vice presidential running mate by Ronald Reagan in 1976 to bolster his challenge against President Jerry Ford. But Schweiker’s faith in the American government seemed deeply shaken by his Kennedy probe, which convinced him “the fingerprints of intelligence” were all over Lee Harvey Oswald.

“Dick made a lot of statements inside the committee that were a lot more inflammatory than anything I ever said, in terms of his suspicions about who killed Kennedy,” recalls Hart. “He would say, ‘This is outrageous, we’ve got to reopen this.’ He was a blowtorch.”

Hart too concluded Kennedy was likely killed by a conspiracy, involving some feverish cabal from the swamps of anti-Castro zealotry. And when he ran for president in 1984, Hart says, whenever he was asked about the assassination, “My consistent response was, based on my Church Committee experience, there are sufficient doubts about the case to justify reopening the files of the CIA, particularly in its relationship to the Mafia.” This was enough to blow other people’s minds, says Hart, including remnants of the Mafia family of Florida godfather Santo Trafficante, who plays a key role in many JFK conspiracy theories. “[Journalist] Sy Hersh told me that he interviewed buddies of Trafficante, including his right-hand man who was still alive when Hersh wrote his book (‘The Dark Side of Camelot’). He didn’t put this in his book, but when my name came up, the guy laughed, he snorted and said, ‘We don’t think he’s any better than the Kennedys.” Meaning they were keeping an eye on Hart? “At the very least. This was in the 1980s when I was running for president, saying I would reopen the (Kennedy) investigation. Anybody can draw their own conclusions.”

Hart, of course, never made it to the White House. But another politician who had been deeply inspired by JFK did — William Jefferson Clinton. And like perhaps every other man who moved into the White House following the Kennedy assassination, he too was curious about finding out the real story. “Where are the Kennedy files?” the young president reportedly asked soon after he went to work in the Oval Office.

And what about the other JFK from Massachusetts, who also met President Kennedy as a young man — John F. Kerry? If he’s elected in November, will he be tempted to launch an inquiry and try to find out what really happened to his hero in Dallas? Hart says he doubts it. “You almost had to go through it like I did with the Church Committee and get all the context. Otherwise, you have to be very careful about falling into the conspiracy category. I at least had some credentials to talk about it. But if Kerry were to bring it up, people would just say he’s wacky, he’s obsessive.” As Hart observes, there are other ways to kill a leader these days — you can assassinate his character.

And so 40 years after the Warren Report, with the country’s political elite still wracked with suspicions about the Kennedy assassination, yet immobilized from doing anything about it by fears of being politically marginalized, and with the media elite continuing to disdain even the most serious journalistic inquiry, the crime seems frozen in place. It is now up to historians and scholars and authors to keep the spirit of inquiry alive.

For decades the only public critics of the Warren Report were a heroic and indomitable band of citizen-investigators — including a crusading New York attorney, a small-town Texas newspaperman, a retired Washington civil servant, a Berkeley literature professor, a Los Angeles sign salesman, a Pittsburgh coroner — all of whom refused to accept the fraud that was perpetrated on the American people. Undaunted by the media scorn that was heaped upon them, they devoted their lives to what powerful government officials and high-paid media mandarins should have been doing — solving the most shocking crime against American democracy in the 20th century. Their names — Mark Lane, Ray Marcus, Harold Weisberg, Sylvia Meagher, Vincent Salandria, Mary Ferrell, Penn Jones Jr., Cyril Wecht, Peter Dale Scott, Jim Lesar and Gaeton Fonzi, among others — will find their honored place in American history. It is these everyday heroes, and their successors, whose best work will some day come to replace the heavy, counterfeit tomes of the Warren Report.

Dave Reuben and his team in the district attorney’s office were stunned by Jones’s sudden flight. They thought the timing of his escape was suspicious, prompted not just by the imminent publication of the New West expose but also by their own investigation. Somebody in the Hall of Justice had clearly tipped off the temple. “We were ready for grand jury indictments; we were this close,” said Reuben. “And [DA] Freitas would’ve had to go along with it, because he had no other choice. The next thing I know, I get a phone call in the middle of the night. ‘Guess what, he’s gone.’ Jones is gone, and the temple is packing up and getting ready to join him. I remember, we had a meeting in the office, and we said, ‘Somebody snitched us off.’”

In the fall of 1977, as Jim Jones hunkered down in Guyana’s steaming tropical wilderness with his flock of more than 1,000 souls, disturbing reports about the “utopian” community began filtering back to the Bay Area. But political supporters like Harvey Milk, newly elected to the board of supervisors, stuck by the increasingly fanatical leader, out of fear, expedience, or stubborn loyalty. In December 1977 Milk wrote to Joseph Califano, President Carter’s secretary of health, education, and welfare, protesting HEW’s decision to stop forwarding Social Security checks to elderly temple members in Guyana — a key financial pipeline for Jones. “Peoples Temple,” Milk informed Califano, “[has] established a beautiful retirement community in Guyana, the type of which people of means would pay thousands of dollars to patronize.”

Other icons of the Bay Area left, including Angela Davis and Huey Newton, also continued to rally around Jones. Longtime Black Panthers attorney Charles Garry agreed to represent the preacher in his legal battles. Garry became an aggressive mouthpiece for the temple back in the United States, telling the press, “There is a conspiracy by government agencies to destroy the Peoples Temple.” Privately, Garry began to question Jones’s mental stability, but he kept his doubts to himself. After visiting Jonestown in October 1977, the radical lawyer announced, “I have seen paradise.”

In reality, the Jonestown “paradise” was a nightmarish Third World police state. Everyone but the youngest and oldest were forced to work like mules from dawn to dusk in the sweltering fields, scratching out a living from the wild jungle terrain. Chronically short of food, residents struggled to keep their weight up with starchy meals like cassava bread drenched in brown syrup and rice soaked with gravy. Families and lovers were forced to live apart, relatives were pitted against one another, neighbors were ordered to inform on each other.

After dinner, the exhausted community was forced to assemble for interminable “emergency meetings” and listen to Jones’s increasingly mad ravings late into the night. Punishment was swift for those who nodded off. One evening a 60-old father of five named Charlie, worn out from fieldwork, slumped to the ground. An incensed Jones commanded Charlie’s son to wrap a boa constrictor around his father’s neck, releasing him only after the poor man’s face was turning red and he had humiliated himself by pissing his pants.

Jones and his heavily armed security team kept the community in a state of terrorized obedience. Minor infractions could send malefactors of all ages, even children, to the dreaded Box, a stuffy underground cubicle where they could be held for days. Those who dared to dissent were dispatched to the medical unit, where they were forcibly drugged and kept in a zombified state indefinitely.

While his followers lived hungry, Spartan lives, Emperor Jones resided in relative splendor in a cottage well stocked with electric appliances, delicacies like hard-boiled eggs, snacks, and soft drinks, and a cache of medications that he had expropriated from his aging and feeble residents. His drug supplies were endless.

The temple leader had been dependent on amphetamines, sedatives, and other drugs for years. Jim Jones Jr. remembered that as far back as the family’s days in Redwood Valley, his father kept a tray of white liquid in the refrigerator and would fix syringes with the fluid and inject himself. One time he overdosed, flailing around on the floor, and the worried kids were told that their father had suffered a heart attack. But years later, after working in a hospital, the younger Jones came to realize his father had displayed the symptoms of a speed addict.

In the glorious isolation of Jonestown, under his tropical canopy, Jones surrendered fully to his drug-fueled manias. He created an Orwellian dystopia and forced his captive followers to live in it. The nights were the worst, as the jungle’s dark silence was broken by a ghastly soundtrack of howler monkeys’ screechings and Jones’s sudden eruptions over the loudspeakers. Father’s voice was everywhere: in the huts, outhouses, fields. There was no getting away from his sleepless rants.

“White Night!” Father would yell in the deepest black of night, jolting his followers from their exhausted slumber. “White Night!” Residents were rushed toward the glaring lights of the pavilion, the elderly shuffling along in a daze, the children crying. When they were all gathered there, Jones — spazzy and hot-wired on speed — told them that the US government was about to pounce. They had to act quickly.

“Hear that sound?” Father told them. “The mercenaries are coming. The end has come. Time is up. Children . . . line up into two queues, one on either side of me.”

The guards stood solemn vigil over a large vat next to Jones.

“It tastes like fruit juice, children. It will not be hard to swallow.”

The White Night drill. It was terrifying but not real. Until the day it was.

Excerpted from “Season of the Witch” by David Talbot. Copyright 2012 by David Talbot. Excerpted by permission of Free Press, a division of Simon & Schuster. All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.

Reuben had been recruited by San Francisco District Attorney Joe Freitas after the DA was swept into office with progressive mayor George Moscone in 1975. Like Moscone, Freitas was a Kennedyesque Catholic politician with wavy-haired, Mediterranean good looks. Raised in a Portuguese family in the Central Valley, Freitas had served in all the stations of the liberal cross, including the National Urban League and Common Cause, before running for San Francisco DA at the age of 36. Brimming with youthful self-confidence and political ambition, the new district attorney created a special prosecutions unit, filling it with young “red hots”—as Reuben described himself and his gung-ho colleagues. Freitas promised his mod squad a free hand in going after city corruption. “He told us there were no holds barred: dirty cops, dirty politicians, payoffs,” recalled Reuben. “Joe said, ‘I don’t care who it is, you go after them.’”

Freitas recruited crusading lawyers and investigators from all over the country for his new unit. Reuben and his crew came in with guns blazing, targeting the deep corruption in the San Francisco police force, including payoffs to cops by the skin trade moguls in North Beach. But Reuben soon found that the San Francisco justice establishment was more impregnable than he had imagined.

Coming from Chicago, where he had broken in as an investigator for the state attorney’s office, pursuing corruption in Mayor Richard Daley’s permanent regime, Reuben thought he had seen it all. But the San Francisco cop culture proved an even tougher nut to crack. “I thought that coming from Chicago, I knew old-boy’s networks,” he said, “but this was really something out here. It’s a true old-boy’s network. All the cops and prosecutors know each other, they’re all friends and family, they all went to the same parochial schools. And here we all come into the DA’s office: we were all in our twenties, and we’re all ballbusters. I mean, I took on the Daley machine. We didn’t care, we were going to investigate everybody. Well, it turns out that you don’t do that in San Francisco — not unless you have the inside support. And I’m Jewish, from Chicago. So I was more outside than you can ever imagine.”

By the time that Al and Jeannie Mills walked into his small office at the Hall of Justice in early 1977, Reuben and his team were beginning to feel demoralized. They had won some minor victories in their campaign against police corruption, but they were feeling increasingly isolated—not just within the Hall of Justice, where police inspectors feared and hated them, but within the DA’s office itself, which was bitterly divided over Freitas’s progressive reign. But the Peoples Temple investigation could make up for all the frustrations, Reuben realized. It was the kind of case that could make an investigator’s career.

The Millses, who defected from the Peoples Temple in 1976, told Reuben and his team that Jim Jones was a violent, drug-crazed despot. They accused him of ordering the murders of disaffected members and subjecting others to savage beatings, including their 16-year-old daughter, who was whipped so severely, according to Al, “her butt looked like hamburger.” The couple — who had changed their names from Elmer and Deanna Mertle to evade temple enforcers — told the investigators that Jones forced members to turn over their property and possessions to the church and confiscated their welfare and Social Security checks. They said Jones had also built his organization into a potent political machine, manipulating elections and politicians and working his way into the inner circles of power in San Francisco.

Reuben and his colleagues immediately recognized how explosive the Millses’ charges were. “At the time, Jim Jones was an acknowledged civic leader,” recalled Reuben. “I mean, he was the Second Coming in this city, bringing together black and white, rich and poor. He had presidents and governors and congressmen kissing his ring. And Joe Freitas was one of those people.”

Reuben and the chief of the special prosecutions unit, a former US prosecutor named Bob Graham, girded their loins and walked into their boss’s office to present the accusations against the Peoples Temple. As Reuben and Graham itemized the charges to Freitas and his number two man, Danny Weinstein, the room grew tense. “We lay it all out, and you could’ve heard a pin drop,” Reuben said. “And then Joe looks at us and says, ‘What, are you guys nuts?’”

Freitas heatedly pointed out to his special prosecutions team that people walked into the DA’s office all the time with wild charges and personal grudges. “You guys can’t just buy this stuff,” Freitas admonished them.

Reuben and Graham were incensed. The hard-charging, windmill-tilting DA who had hired them — and told them they had carte blanche — was now suggesting that they back off what could be the hottest case they’d ever worked. They immediately knew what was going down. They’d read the newspapers and knew all about the furious allegations swirling around the city: that Jim Jones and his zombie flock had stolen the election for Mayor Moscone, and had worked hard for Freitas too.

“We were pissed,” Reuben recalled later. “It was too dynamic for us not to dig into. All the names mentioned — Willie Brown, Dianne Feinstein, George Moscone — the whole gang was in there, I’m sure. And, of course, it was obvious to us — we’re not idiots — Joe was in the middle of the thing. He knew that if we started doing this thing, his career might be affected.”

Freitas was too politically savvy to simply shut down the Peoples Temple investigation. He knew that his angry investigators’ suspicions could wind up in the press. So he gave his special team just enough leash to quietly look into the Millses’ accusations. And to make sure that Reuben and Graham did not dig too deeply, Freitas appointed a young deputy named Tim Stoen as his liaison on the case.

Reuben did not know much about Stoen. The deputy DA, who wore horn-rimmed glasses and three-piece suits, was a straitlaced loner. “He was a nerdy kind of guy,” Reuben recalled. “Very bright, well spoken. We thought he was one of us, a reformer. But we joked about it, because he seemed too idealistic. He really wasn’t friendly with anybody, just did his own thing.”

As Reuben and his team dug deeper into the Millses’ hair-raising stories about the Peoples Temple, the allegations were checking out. Interviewing other defectors and anxious relatives of temple members, the investigators soon learned how fearful these people were of reprisals from Jones’s security guards — all of whom, Reuben discovered, had long rap sheets. Reuben promised his witnesses that he would protect their anonymity. But when he and his colleagues casually referred to their partner on the case, Deputy District Attorney Tim Stoen, the witnesses looked stunned. “Tim Stoen?” said one defector to Reuben, with panic in his eyes. “He’s Jim Jones’s top legal advisor.”

A chill ran up Reuben’s spine when he heard this. Afterwards he and Bob Graham stumbled in a daze over to a cop bar across the street from the Hall of Justice, to compare notes. What the hell was going on? The question hung over them like a noose as they hunched over their drinks. “So now we’re figuring, Is Stoen a plant? Does Freitas know who he is, or did this guy just weasel his way in? Does this all go back to Jones? Even before this, we didn’t know who to trust in the office. But now we’re really paranoid, because we don’t know who’s calling the shots.”

The two investigators marched into Freitas’s office to confront their boss. “We blew up,” recalled Reuben. “We said, ‘What’s going on here? Are we being made patsies in this whole thing?’”

Freitas acted surprised. “He said, ‘Are you guys sure?’ And this and that, like he didn’t know anything about Stoen.” But the investigators realized that Stoen was far too cozy with their boss for him not to have known.

Joe Freitas would later tell the press he had no idea that Tim Stoen was Jones’s right-hand man when he hired him; that he had simply plucked his resume out of the slush pile. But in truth, the Peoples Temple, which had contributed money and campaigned for Freitas, engineered Stoen’s insertion into the DA’s office as a political reward for its efforts. And in a brazen move to cover up the voter fraud committed by the temple during the 1975 election, Freitas put the temple’s lawyer in charge of the investigation. In doing so, he ensured that San Francisco would never find out who’d really won the mayoral election. Stoen brought in Peoples Temple clerical volunteers to help with his politically sensitive probe. The foxes had free run of the henhouse, and they left only feathers.

Three years later, after the name Jim Jones had gone down in infamy, state and federal investigators finally began looking into the shady election. When they asked for all the rosters showing who voted, the city’s deputy registrar of voters went searching for the records in three locked vaults where they were kept. All the records were missing.

After they found out about Stoen, Reuben and Graham began taking their files home at night, no longer sure that they could protect the confidentiality of their Peoples Temple witnesses, some of whom feared for their lives. The investigators’ suspicions were well founded. Stoen, it turned out, was literally a sleeper in the DA’s office. He often spent the night there, though he had a residence on Page Street, giving him free access to the office’s most sensitive documents for almost a year. Stoen and his wife, Grace, whom he had brought into the temple, enjoyed “a free romp through the place after hours,” one source reported. Freitas later shrugged off his deputy’s after-hours routine. “He was a hard worker,” the DA explained, and after toiling late into the night he often needed to avail himself of his office couch.

Excerpted from “Season of the Witch” by David Talbot. Copyright 2012 by David Talbot. Excerpted by permission of Free Press, a division of Simon & Schuster. All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.

Jones’s flock, ignored and scorned by society, was electrified by the preacher’s vision of a new Eden. Everybody was exalted in his services, even the lowliest recovering drunks and addicts. “He made us feel special, like something bigger than ourselves,” said one temple member. “Total equality, no rich or poor, no races,” said another. “We were alive in those services,” testified one more. “They had life, soul power.”

Jones — an oddball and renegade his entire life, someone who never felt at home in his own skin — had found his identity by taking on a black persona. He saw himself following in the footsteps of Malcolm and Martin, leading “his” people out of bondage and into the promised land.

In reality, Jones maintained a racial hierarchy within the organization. While church membership was primarily black, the 37-member planning commission, as Jones called his leadership council, was dominated by white women — at least six of whom were his sexual conquests and firmly under his sway. “When people talk about my father manipulating black people, that’s true,” said Jim Jones Jr., the preacher’s black adopted son. “It was politically advantageous for him to give me his name.”

There was something exhibitionistic about the way that Jones and his wife treated their black son. “I was the chosen one,” he said. “I was more loved in my family than the other kids, even their biological son, Stephan. I remember Mom wiping charcoal off a dirty pot one day and rubbing it all over her face — to show that we were all black.”

Jones soon learned that his control over a well-organized, mixed-race army of some 8,000 dedicated followers gave him major stature with San Francisco’s liberal elite. Redevelopment had bulldozed the Fillmore’s political power into the ground. But now this strange white man with the hipster shades, Indian-black hair, and cadences of a black Bible-thumper seemed to be erecting a new political power line into the rubble-strewn, crime-ridden no-man’s-land. Jones could be counted on to deliver busloads of obedient, well-dressed disciples to demonstrations, campaign rallies, and political precincts. The city’s liberal Burton machine — run by congressional powerhouse Phil Burton — quickly identified the Peoples Temple juggernaut as a potentially game-changing ally in its long battle to take over city hall.

It was Burton ally Willie Brown – a rising force in California’s state capital — who first recognized that Jones’s organization could play a pivotal role in his friend George Moscone’s run for mayor. Moscone, a charming and handsome state legislator, had electrified San Francisco progressives with his campaign for city hall. A champion of gays, women, minorities, tenants and organized labor, Moscone was locked in a tight race with a pack of opponents led by conservative realtor John Barbagelata, whose campaign evoked a nostalgia for an older San Francisco, when it was ruled by traditional Catholic values. A meeting was set up between Jones and Moscone in the office of Don Bradley, the candidate’s veteran campaign manager. Bradley was initially cautious. “I was a little leery we were getting into something like the Moonies,” he later recalled. But after he looked into the temple’s campaign history and saw how effective it was in delivering victories, Bradley enthusiastically embraced Jones’s volunteer army. Nearly 200 temple members showed up at Moscone headquarters, fanning out to campaign in some of the city’s toughest neighborhoods, and helping the candidate finish first in the November 1975 election.

In the December runoff between Moscone and Barbagelata, Peoples Temple went even further to secure victory for its candidate. On the eve of the election, Jones filled buses with temple members in Redwood Valley and Los Angeles and shuttled them to San Francisco. Security at polling places was lax on Election Day, and many nonresidents were able to cast their ballots for Moscone, some more than once. “You could have run around to 1200 precincts and voted 1200 times,” said a bitter Barbagelata later, after losing by a whisper of a margin. But he was not the only one who claimed that the Peoples Temple stole the election for George Moscone. Temple leaders also claimed credit.

“We loaded up all 13 of our buses with maybe 70 people on each bus, and we had those buses rolling nonstop up and down the coast into San Francisco the day before the election,” recalled Jim Jones Jr. “We had people going from precinct to precinct to vote. So could we have been the force that tipped the election to Moscone? Absolutely! Slam dunk. He only won by 4,000 votes. I’m sorry, but I’ve got to give my father credit for that. I think he did the right thing. George Moscone was a good person; he wanted what was best for San Francisco.”

Jim Jones made sure that George Moscone never forgot his political debt to Peoples Temple. The man who began his term in city hall with a ringing promise to make San Francisco a beacon of enlightenment would start off his administration with a wretched burden on his back. The mayor could never rid himself of the stench of contagion that Jones brought with him, and as time went by, the power-hungry preacher only sunk his fangs in deeper. The pastor was a wickedly smart reader of a politician’s character, and he knew that the way to enchant Moscone was with young women, not money. When it came to bribing politicians, the temple leader had ample supplies of both. Jones bragged of supplying Moscone with black female members of his congregation. Jim Jones Jr. remembered the mayor as “a party guy. He’d always be there at temple parties with a cocktail in his hand and doing some ass grabbing.”

Temple insiders talked about how Mayor Moscone was one of the politicians under the control of “Father.” They gossiped about the night that the mayor had fallen into Jones’s hands. “Moscone was known to be a boozer; he liked to drink at parties,” recalled temple member Hue Fortson, now a pastor in Southern California. “One night there was some sort of temple event that the mayor attended. The next morning I heard that Jones phoned Moscone and told him it was a pleasure to see him the night before and to see him having such a good time. ‘But I want to let you know that the young lady you went off with is underage,’ Jones told him. ‘Now don’t worry, Mayor, we’ll take care of you — because we know that you’ll take care of us.’”

Jones might have made up the stories of sexual blackmail. He was known to concoct outlandish tales. “Jim was always bragging that he had sexually compromising information about politicians,” remembered Terri Buford, an on-again, off-again mistress of Jones who belonged to the temple’s inner circle. “But you never knew if what he said was true. He once told me that Willie Brown was sexually attracted to him. He just made stuff up.”

Whether or not Moscone was sexually compromised by Jones, he was certainly politically ensnared. The mayor initially resisted the temple’s efforts to insert its members throughout city government. And when Jones himself pushed for a high-level appointment, Moscone at first tried to appease him with a harmless post on the human rights commission. But the temple leader insisted on a position that had more clout, and the mayor decided he was in no position to alienate Jones. In October 1976 Moscone announced that he was naming Jones to the San Francisco Housing Authority, which oversees the operation of the city’s public housing. The agency, the largest landlord in the city, was a notorious maze of corruption, and it provided Jones’s organization with ample opportunity for shady self-dealing. A few months later, Moscone pulled strings to promote Jones, making him chairman.

Jones swept into the normally tedious meetings of the housing commission like a banana republic despot, surrounded by an entourage of aides and grim-faced security guards. Looking stern and inscrutable behind his aviator sunglasses, Jones ran the meetings with scripted precision while sipping a frothy white drink brought to him by a hovering retainer. The audience, packed with elderly black temple worshippers, erupted into wild cheers at his most routine pronouncements. Temple enforcers roamed through the meetings, keeping a watchful vigil, and even blocking people from entering the bathroom while Jones was inside.

Jones used his position to take possession of public housing units and install temple members in them, and he put other followers on the housing authority payroll. The preacher was building his own power base within city government. “He was using his power to recruit members and to put the hammer on people,” said David Reuben, an investigator for San Francisco District Attorney Joseph Freitas, another politician under Jones’s sway. “He had a lot of authority.”

“Jim Jones helped George Moscone run this city,” said Jim Jones Jr., a chillingly matter-of-fact assessment of the temple leader’s creeping encroachment in San Francisco.

Political leaders, aware of Jones’s ability to deliver — or manufacture — votes, lined up to pay tribute to the preacher. He worked his way into the good graces of officials high and low — most of them Democrats, since that was the party in power in California and San Francisco in the mid-1970s. But Jones was also happy to exchange mutually complimentary correspondence with the offices of Ronald Reagan and statesman Henry Kissinger.

During the 1976 presidential campaign, Jones wangled a private meeting with Jimmy Carter’s wife, Rosalynn, at the elegant Stanford Court Hotel on Nob Hill, arriving with a security contingent that was larger than her Secret Service squad. Later Jones accompanied Moscone and a group of Democratic dignitaries who climbed aboard vice presidential candidate Walter Mondale’s private jet when it touched down at San Francisco International Airport.

Governor Jerry Brown sang the preacher’s praises. Congressman John Burton, Phil’s brother, lobbied the governor to appoint Jones to the high-profile board of regents, which oversaw California’s sprawling public university system. San Francisco Supervisor – now U.S. Senator — Dianne Feinstein accepted an invitation to lunch with Jones and to tour Peoples Temple.

But no political figures were more gushing in their praise of Jones than Willie Brown and Harvey Milk, San Francisco’s rising tribune of gay freedom. Milk, a perennial candidate for office until he finally won a supervisor’s seat in 1977, aggressively sought Jones’s political blessing. “Our paths have crossed,” Milk wrote Jones during an earlier campaign for supervisor, in a letter filled with the kind of awed reverence that the cult leader demanded from his followers. “They will stay crossed. It is a fight that I will walk with you into . . . The first time I heard you, you made a statement: ‘Take one of us, and you must take all of us.’ Please add my name.”

Not content to hear dignitaries whisper flatteries into his ear, Jones staged a testimonial banquet in his own honor and demanded that politicians in his debt offer him public tribute. On the evening of September 25, 1976, the Peoples Temple headquarters on Geary Boulevard was converted into a formal dining hall with linen tablecloths and floral arrangements. At the head table sat Mayor Moscone, District Attorney Freitas, and Assemblyman Willie Brown, who acted as the evening’s exuberant master of ceremonies. As he introduced the man of the hour to the overflow audience, Brown reached new heights of shameless, ass-kissing puffery. “Let me present to you,” Brown roared, “a combination of Martin King, Angela Davis, Albert Einstein . . . Chairman Mao.” By the time Jones rose to tumultuous applause, he seemed likely to walk on water.

Privately, San Francisco political leaders expressed doubts about Jones and his strange church. One day a friend of Milk’s named Tory Hartmann dropped off some boxes of campaign brochures at Peoples Temple, so that Jones’s army could distribute them. Hartmann was immediately unnerved by the uptight, high-security atmosphere inside the temple, where sentries stood at attention outside each room, like the palace guards in the Wicked Witch’s castle. “This is a church?” Hartmann said to herself. Later, after she sped back to the Castro and told Milk about her bizarre experience, the naturally cheery politician turned deadly serious. “Make sure you’re always nice to the Peoples Temple,” he told her. “They’re weird and they’re dangerous, and you never want to be on their bad side.”

Cleve Jones, a young Milk aide, accompanied him to Peoples Temple for a couple of Sunday services. “Harvey told me, ‘Be careful, they tape everything.’ Everyone knew Jim Jones was creepy, everyone knew he was a megalomaniac. But everybody also saw this church full of black and white people — black people from the Fillmore who had been subjected to apartheid-like policies and seemed to finally be getting some respect.”

Members of Moscone’s staff were also beginning to hear troubling reports about Peoples Temple. One day mayoral aide Dick Sklar suggested to his family maid — an African-American woman who had followed the Sklars to San Francisco from Ohio — that she attend a Sunday service at Peoples Temple. “I didn’t know anything about it,” Sklar said, “but she was a churchgoing woman, and I thought she might like it. Afterward she came back and said it was the scariest place she’d ever been. They searched her, asked her questions. I had no idea.”

Moscone himself could not ignore how peculiar his political ally was. “I was at every meeting that Jim Jones ever attended with the mayor,” said Moscone press secretary Corey Busch. “I can tell you that after every one of those meetings, the reaction was, ‘This is one weird bird.’ He always wore the dark glasses. You couldn’t predict Jonestown, but he was definitely weird. In retrospect, maybe we should have seen that, but we didn’t.”

Excerpted from “Season of the Witch” by David Talbot. Copyright 2012 by David Talbot. Excerpted by permission of Free Press, a division of Simon & Schuster. All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.

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