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.

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?

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.

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?