Over the past century or more, there have been quite a few breakaway Mormon sects scattered across rural North America, small groups led by self-appointed prophets who rejected the Church of Jesus Christ of Latter-day Saints’ decision to disavow Brigham Young’s famous doctrine of “plural marriage” in the 1890s. For the most part these splinter sects have been left alone, even (or especially) in a place like Utah, where the mainstream Mormon Church still dominates the political and cultural landscape. In the larger picture of American society and religion, such fundamentalist Mormon groups have been nothing more than tiny, stagnant backwaters of belief. All of them, that is, except one.

That group is the Fundamentalist Church of Jesus Christ of Latter-Day Saints (usually called the FLDS Church), a multi-million-dollar business enterprise that owns large chunks of remote real estate in Utah, Arizona, Colorado, South Dakota, Texas, Oklahoma and northern Mexico. FLDS-owned companies made the O-rings that failed in the Space Shuttle Challenger in 1986 (although the failure was likely a result of flawed NASA specifications), have managed and run major construction projects all over the Western states and have installed the lighting in numerous Las Vegas casinos. For many years the FLDS Church has been dominated and operated by a man named Warren Steed Jeffs, who “married” more than 60 women and girls, some as young as 12 years old, and has repeatedly been accused of molesting children of both sexes, including his sisters, his daughters and his nieces and nephews.

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Jeffs made the FBI’s Most Wanted list in the mid-2000s, spent several years as a fugitive, and was ultimately convicted on two counts of sexual assault against children by a Texas jury in 2011. During Jeffs’ two trials (an earlier conviction in Utah was thrown out), Mormon fundamentalism became an object of cultural fascination, inspiring the HBO series “Big Love.” That has faded, and Jeffs is almost certain to spend the rest of his life in prison. But as filmmaker Amy Berg’s new Showtime documentary “Prophet’s Prey” makes clear, the FLDS empire of rape and misogyny and child labor and relentless ideological and psychological domination appears to go on much as before. Despite his isolation and his precarious mental condition, Jeffs continues to command the devotion and obedience of his 10,000 or so followers from behind bars, like an old-time Mob boss with a direct line to God.

There was nothing especially strange or nefarious about the way mainstream Mormons and local law enforcement chose to ignore fundamentalist groups like the FLDS, although we can say in retrospect that it led to dire consequences. From the point of view of the LDS Church leadership in Salt Lake City, engaging with the disgruntled offshoots in any way was a no-win situation. For the last 60 or 70 years, Mormons have struggled to reposition their faith as a modern religious institution rather than a kooky artifact of pioneer America and the Second Great Awakening. Renegade groups who still practiced polygamy and dressed their flocks of sister-wives in hand-sewn “Little House on the Prairie” dresses and World War I hairdos weren’t helping. If the public largely viewed Mormons as freakazoids in clip-on ties with kinky underwear, who might well be practicing plural marriage in secret, then any attention paid to the throwbacks would only heighten the confusion.

This subject makes private investigator Sam Brower a little uneasy when I bring it up. Brower, who is himself a Mormon, is a sunburned, silver-haired, middle-aged man with the distinctive air of a Westerner who has spent his life outside. At breakfast in a trendy coffee shop in lower Manhattan (where I met him and Amy Berg, the filmmaker), he orders a Diet Coke amid a veritable forest of lattes and cappuccinos and chai. (I did not ask whether he observes the Mormon prohibition on caffeine.) When he moved to Utah from California some years ago, Brower agrees, he noticed “a sense of apathy” around Mormon fundamentalism in the Beehive State. “It was like they were just part of the landscape: You leave us alone, we’ll leave you alone.” But why, he continues, was this issue seen as the sole responsibility of the LDS Church, which had renounced polygamy and excommunicated every fundamentalist resister it could identify? Why hadn’t Catholic bishops and Jewish rabbis spoken out? Why had county sheriffs and attorneys general and federal prosecutors almost unanimously looked in the other direction?

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Some of those questions answer themselves: Jews and Catholics felt no historical or theological responsibility for bands of weirdos in the wilderness who pronounced themselves the true heirs to Joseph Smith and Brigham Young. But if Brower feels defensive about outsiders’ attempts to connect mainstream Mormons to the wide-ranging criminal activities of the FLDS Church, by far the largest and most powerful of all Mormon breakaway groups, he has unmistakably earned that right.

Along with author and journalist Jon Krakauer (and arguably now Berg, whose documentary features both of them and is based on Brower’s book of the same title), Brower has done more to expose the enormous but almost invisible criminal empire built by Warren Jeffs than anyone in the world. Furthermore, in the larger context of social and religious history, Brower is clearly correct that the disturbing story of the Jeffs family and the FLDS Church reflects issues that go far beyond the contradictions of Mormon theology and the weirdness of the American West.

We can easily find a troubling parallel in today’s front pages, and as Brower will tell you, it’s not nearly as far-fetched as it sounds. You don’t have to approve of religion in general or the LDS Church to see that blaming the faith of Mitt Romney and science-fiction author Orson Scott Card and New York Yankees outfielder Jacoby Ellsbury for the apocalyptic extremism and mind-control techniques and vicious sexual predation of Jeffs’ isolated cult group is a lot like blaming Muslims in general for the 9/11 attacks or the gruesome crimes of ISIS. There’s an obvious historical connection that no one denies, but the two things are not the same.

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After Brower tells me twice that he fears that the FLDS saga might end in catastrophic violence, and that he feels certain that Jeffs’ followers would kill or die for him, I ask how he sees the differences between the FLDS and ISIS. Both groups have sought to pursue prophetic religious teachings to their ultimate extreme, and both have constructed a throwback social order based on male domination, female subjugation, forced marriage and the rape and sexual enslavement of children. If Warren Jeffs had the guns, the territory and the freedom that ISIS possesses, how far would he go?

Brower chuckles in a way that suggests he has asked himself the same question. “I would say the difference between them is an AK-47,” he says. “Warren doesn’t have those, and instead of using AK-47s, he uses people’s fear for their salvation. Where my fear comes from is that we know that there's armed security there [on the various FLDS compounds]. They've got weapons, and they've had tactical military-type training. So we know that they're capable of that. And I am 100 percent certain that if and when the time comes, if Warren told them to die at their posts, and the FBI were starting to come in or something, they would die for him. No doubt about it.”

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I have to issue a warning to anyone who might see “Prophet’s Prey,” which begins its theatrical release this week in New York and will premiere on Showtime next month. It’s a fascinating work of investigative journalism and cultural spelunking – and it features perhaps the most disturbing minute of audio recording you will ever hear. Berg and Brower decided to include the opening segment of a tape Jeffs had made documenting the consummation of his “marriage” to the youngest of his “spiritual brides,” who was then 12 years old. In other words, it’s a recording of a middle-aged man raping a little girl, while an uncertain number of Jeffs’ other wives stand by, ready to assist. Once heard, it cannot be unheard, but Berg insists it was important.

“Sam told me early on that even after Warren had been arrested and went on trial, people in the FLDS community didn't believe any of it,” Berg says. “We talked about it many times: How much of the tape to use and where to put it and all of that. But I felt that the jury heard it, and it was on the record. If there was any chance that people that hadn't heard it before could hear this, it would shed some light. And I think it was a good decision, because since we played the film at Sundance in January, close to 100 women have escaped [from the main FLDS settlement in southern Utah]. Sam is getting those calls all the time, helping those women find food and shelter.”

“Amy was very careful with that tape,” Brower says. “There’s much more of it. It’s much more graphic. That’s only one rape. The evidence produced in Texas was about an hour and a half, different recordings. And the jury – literally after 10 minutes, just about every member of the jury had their headphones off, and their face in their hands, just sobbing. You know, when Jon Krakauer talked about the case on CNN, not only did the people out in Short Creek [Utah] not believe it, the rest of the world didn't believe it either. People said Jon was lying or exaggerating. ‘No, that could never happen! They’d go and arrest him!’ I think it was necessary to put that little taste of it in there so people could know, yeah, it really is true.”

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While Warren Jeffs’ long career as a serial abuser and rapist created lurid headlines, and ultimately landed him in prison, the real story of the FLDS Church is at least as much about money and power as about sex crimes. Brower and Berg only scrape the surface of those issues in a 90-minute documentary, but it’s not fanciful at all to compare the interlocking tangle of FLDS-owned shell corporations, “shelf corporations” and quasi-legitimate businesses – carefully established in different jurisdictions, and all designed to funnel cash upward to Jeffs and his closest associates – to the operations of old-school organized crime. FLDS leaders (the functional head is presumably Lyle Jeffs, Warren’s brother, himself now a fugitive from justice) shuffle hundreds of millions through dozens of bank accounts in several states, pay fictional salaries to employees who actually work 20-hour days for almost nothing, and compel the children of church members to work as virtual slaves.

In fact, if there’s one thing that might lead bring down this vast but little-known evil empire, which has combined two American traditions – the end-times religious cult and the organized crime family – in unique and sinister fashion, it is more likely to be the repeated violations of child labor laws then the cascade of rape and abuse charges. “That’s how the majority of the FLDS Church’s money is made, through the slave labor of children,” Brower says. As we see in the film, when the FLDS-owned pecan groves in Utah are ready for harvest, the church doesn’t hire migrant laborers. It has a more cost-effective solution: Close school for a week and send the kids out to pick nuts for no pay. (Boys and girls are kept apart, to be sure.)

Largely as a result of Brower’s willingness to wade through tedious financial documents and court records, the federal Department of Labor has spent three years investigating and fining various FLDS-owned businesses and following the money trail back to the church itself. Lyle Jeffs and another brother, Nephi Jeffs, face contempt charges, and the church itself faces a potentially crippling federal suit. Among the numerous women who have recently left the church is Charlene Jeffs, Lyle’s only legal wife, an extremely high-level defector. She has apparently been talking to the Justice Department.

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Brower worries about the fact that Warren Jeffs is “in really bad shape” in his Texas prison cell, both mentally and physically. If Jeffs believes that his brothers and followers have failed him, Brower says, he could decide, “OK, this is it: I’m going to push the envelope as far as it will go.” But through many years of work the Mormon private eye has compelled the media, the public, the government and, yes, his own faith to confront one of the most insidious and destructive religious sects in American history, which was hiding in plain sight and tolerated for far too long. He admits to some satisfaction, with a curt nod and a swig of Diet Coke: “There’s some good things happening.”

“Prophet’s Prey” is now playing at the IFC Center in New York, and opens Sept. 25 at the ArcLight Hollywood in Los Angeles, with a national rollout to follow. It will premiere in October on Showtime.