What happened when Michael Quinn challenged the history of the church he loved.

Quinn told friends that he did not want anyone to lobby on his behalf. He himself did not even stay in town. He went to San Diego to give the keynote address for the annual conference held by Affirmation, a support group for gay and lesbian Mormons, and he stayed in California for several days afterward. At the conference, he spoke about the history of same-sex relationships in the church and the shifting attitudes toward them on the part of Mormon leaders. On Sept. 30 he called Hanks to ask what the court had decided. Hanks told him he had been excommunicated, and said that the court lasted six hours. Quinn was shocked that it took that long. Later he was told that despite his request that no one speak for him, a friend had attended and done just that, playing recordings of Quinn’s presentations at past Sunstone Symposia and reading excerpts from his writings. (Quinn attempted to reach this friend through a third party before my piece was finished, but declined to give me his name before speaking to him.) This friend, Quinn says, told him that the men on the council disagreed about whether Quinn was an apostate, and that President Hanks finally declared that Boyd K. Packer was pressing him to take action, and they needed to do something.

While Packer’s precise involvement remains a matter of dispute, what little is known hints at his interference. After Paul Toscano was excommunicated, Steve Benson, grandson of the then Mormon prophet, met privately with the apostles Dallin H. Oaks and Neal A. Maxwell, and asked them about—among many other things—the rumor that Packer had something to do with it. Oaks said Packer had met with Toscano’s stake president, and acknowledged that this was a mistake. When Benson asked why no one had stopped him, Oaks allegedly replied, “You can’t stage manage a grizzly bear.” Benson resigned his Mormon membership shortly afterward and became a vocal opponent of the church his grandfather ostensibly led.

In October, the Salt Lake Tribune reported that a threatening phone call had been made to the home of a local man named Michael D. Quinn. (Quinn is known professionally as D. Michael Quinn; the first name on his birth certificate is Dennis.) This other Quinn was not home when the call came, and a baby-sitter answered the phone. She was told to pass along this message: “I’m tired of hearing him criticize the church. He’d better start keeping it to himself. If he doesn’t, I have his phone number and I know where he lives. I’ll come get him. I hate him. He stinks.”

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Following the wave of media attention that greeted the September excommunications, the First Presidency defended what had taken place. They had “the responsibility to preserve the doctrinal purity of the church,” they said, adding that, because Mormon leaders are constrained by confidentiality rules, “the media have relied on information supplied by those disciplined or by their sympathizers.” Similar councils occurred more sporadically over the next few years. A former BYU professor named David Wright was excommunicated in 1994 after publishing a paper arguing that the Book of Mormon was not an ancient text. Paul Toscano’s sister-in-law was excommunicated for her writings about the Heavenly Mother, a controversial aspect of Mormon theology. His wife Margaret, an English professor and feminist who attracted attention from church leaders before her husband did, was excommunicated in 2000.

Disciplinary councils still happen, though they appear to be less frequent, particularly when it comes to apostasy. Once in a while such a case will hit the press. Last month, for instance, the Daily Beast reported that a blogger named David Twede was facing excommunication because of critical pieces he had written about Mitt Romney. This was almost certainly wrong: Romney has plenty of LDS critics, most notably Senate Majority Leader Harry Reid. But the Church’s case against Twede will never be known: After the Daily Beast story, the council was postponed, and a few weeks later, Twede resigned from the faith.

While LDS leaders can be defensive about media attention, sustained criticism from the outside world seems to have an effect. After organizing a massive campaign to pass Proposition 8 and make gay marriage illegal in California, for instance, the church suffered a massive backlash and has since appeared more tolerant toward gay rights activism. Something similar, if more protracted, took place after September 1993. I attended the Sunstone Symposium this past summer, held on the University of Utah campus, and many people I spoke to there said that as Packer’s influence has waned, a more tolerant approach to dissent is taking hold. Earlier this year, Maxine Hanks became the first of the September Six to fully return to the Mormon Church since the conservative outlier Avraham Gileadi was quietly rebaptized almost two decades ago. At Sunstone, Hanks described her path back to Mormonism as a hero’s journey, à la Joseph Campbell. In order to have her blessings fully restored, she had to meet with a general authority at church headquarters. As she entered the building at 47 East South Temple, she happened to pass Boyd K. Packer on his way out. He was in a wheelchair. She was struck by how frail he appeared, and found herself feeling “nothing but compassion and love” for a man who had once seemed like an enemy. She said hello, but he did not recognize her.

In the field of Mormon history the changes are particularly pronounced. In 1997, the acclaimed historian Richard Bushman, who spent much of his career writing on non-LDS topics, began studying his religion again in earnest, and convened an annual seminar that helped attract young scholars who might have pursued other interests. In 2001, a long-standing effort called the Joseph Smith Papers Project received additional funding and became a major draw to those who wished to study the early days of the church. Crucially, much of that project is online—more than anything, the Internet has revolutionized the field. Nowadays, anyone can Google “Mormon polygamy” and learn more than they’d ever need to know about that practice, about its abandonment, the subsequent fallout, and so on. Packer’s notion that those writing church history should share only those things that are “faith-promoting” is not just intellectually offensive now—it has become quaint, the relic of a time when information was not so freely available.

Which has also, it seems, made Michael Quinn’s singular focus on the unspoken parts of the Mormon past less relevant to younger historians, who operate with more freedom and less pressure—and who draw far more interest than their predecessors from the wider world, which has suddenly become fascinated by Mormonism. The field has grown and appears to have moved on, even though the research that Quinn did, and the fights that he picked, were crucial to what has come in his wake.

The timing of his career, which once appeared serendipitous, now seems almost cruel. Following his excommunication, he finished The Mormon Hierarchy: Origins of Power and turned his attention to another scholarly book with deep personal meaning. Same-Sex Dynamics Among Nineteenth-Century Americans: A Mormon Example, published in 1996, argues that same-sex intimacy was much more accepted by early Mormons—including Joseph Smith—than it is today. The book won an award from the American Historical Association, but it brought Quinn more grief in Utah. He contends that a former director of the Mormon Tabernacle Choir had openly romantic feelings for men, and highlights a once hushed-up gay affair from the 1940s between a prominent church leader and a 21-year-old Mormon serving in the Navy. Vern Anderson wrote an AP story about the book, and several Utah papers carried reviews. Quinn got hate mail. At the time, he was grieving the death of his son, who had gone missing and was found weeks later hanging from a tree by an extension cord. It was, Quinn told me, “an awful, awful year.”