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Nestled in an ancient glacial lake bed in the Northern Rockies, Missoula is Montana’s second largest city. It’s bisected by the Clark Fork, a major tributary of the Columbia River, confluent with the Bitterroot River to the southwest and Big Blackfoot to the east. (The latter famously stars in Norman Maclean’s “A River Runs Through It.”). In his latest book, Jon Krakauer describes Missoula as “congenial and picturesque … the kind of community that charms first-time visitors into putting money down on real estate within hours of arriving.”

But something is very wrong here, as Krakauer argues in “Missoula: Rape and the Justice System in a College Town.” Specifically, Krakauer investigates a series of sexual assaults that started in 2010, several of which involved football players for the University of Montana Grizzlies.

Though it was originally slated for a fall release, “Missoula” was rushed to print by Doubleday after Rolling Stone retracted its story about an alleged gang rape at a University of Virginia fraternity, which incited a national debate over false accusations of rape and journalistic responsibility.

As Krakauer explains in the introduction, the spate of rapes in Missoula gained nationwide attention as well, first via articles in the local newspaper, the Missoulian, followed by an investigation by Montana Supreme Court Judge Diane Barz and scrutiny by the U.S. Department of Justice. National publications, including The New York Times and The Wall Street Journal, picked up on the story. The stats and first-hand accounts Krakauer collects here — representing just a few of the at least 80 rapes reported in Missoula over the course of three years — paint a picture of the city, the university, the local police department and the county attorney’s office that’s anything but postcard pretty.

The common thread among the sexual assaults Krakauer covers in “Missoula” is that all are acquaintance rapes among students. A key example is Allison Huguet, a track star entering her junior year at Eastern Oregon University, who was raped by her lifelong friend, Beau Donaldson, a member of UM’s football team, while home in Missoula for the summer. Her story, which is somewhat atypical in that Donaldson was actually arrested and eventually convicted, nonetheless underscores the myriad reasons why so many rape victims are reluctant to go to the authorities. “No more than 20 percent of rapes are reported to the police,” Krakauer points out.

For example, when Grizzlies fans got wind of Donaldson’s arrest, several took to the Internet to rally to the football player’s side. On online forum eGriz.com, one commenter wrote: “It cannot be true, he is from Montana!”

“I know nothing about the facts, but I know Donaldson and I have doubts that rape occurred or that this will stick,” wrote another.

And another: “(C)hicks exaggerate on rape …. Only the people involved actually know what happened. And a lot of people lie.”

Over some 350 pages, Krakauer chronicles the disturbing details of several acquaintance rapes — the victims of which came forward under their real names to speak with him, despite having been variously accused in public of lying or exaggerating or seeking attention. (Other people involved are referred to pseudonymously.)

In one of the most compelling portions of the book, Krakauer — best-selling author of “Into Thin Air” and “Into the Wild,” as well “Under the Banner of Heaven,” which offered a nuanced exploration of violence among some Mormon fundamentalists — recounts the trial of Grizzlies quarterback Jordan Johnson, who was accused of rape. Strangely enough, district attorney Kirsten Pabst left her post as prosecutor in order to defend him. Pabst had previously testified for an alleged rapist at a UM hearing while she was still supervisor of the sexual-assault division at the Missoula county attorney’s office. The latter student was expelled anyway. The former, Johnson, was ultimately acquitted.

After the verdict, Johnson supporters posted to the Missoulian Twitter feed:

“INNOCENT! I would love for the accusers (sic) name to be released and plastered everywhere like Jordan’s was.”

“Now sue her for every last dollar…#Civil retribution.”

Krakauer argues convincingly in “Missoula” that “The legal system stacks the deck more heavily against sexual-assault victims than victims of other crimes. Nevertheless, a small but influential cadre of cops, prosecutors, and academics has developed a set of ‘best practices’ that can help prosecutors win more rape trials, even while scrupulously respecting the rights of the accused.”

Of course, these advancements have often been eclipsed or undermined by stories of false accusations, as is the case of the retracted UVA story. “The Rolling Stone fiasco really discouraged me,” Krakauer said in a recent NPR interview. “(We thought) it’d be a good time to show this book; that… the overwhelming majority, you know, of victims do not lie about rape.”

The tone of “Missoula” is, for the most part, clear and dispassionate, offering level-headed, in-depth reportage. At times, Krakauer’s own disdain for alleged assailants bubbles to the surface. For example, an accused rapist, “Calvin Smith” (a pseudonym) who breaks down in tears “blubbered like a child”; the same accuser’s friend cackles, while testifying, “as if he were playing Beavis to Smith’s Butt-Head.” Such descriptions seem gratuitous; in word and deed, Smith already comes off as something worse than a butt-head.

Quoting a Jezebel article about the city written by Katie J.M. Baker titled “My Weekend in America’s So-Called ‘Rape Capital,'” Krakauer writes that 80 rapes in three years appears to be “on par with national averages for college towns of Missoula’s size.” And indeed, Krakauer confirms this statistic with the FBI. In a December 2014 report, the Department of Justice estimated that 110,000 women between the ages of 18 and 24 are raped each year.

“Rapists rely on the silence of their victims to elude accountability,” Krakauer writes. “Simply by recounting their stories and breaking that silence, survivors of sexual assault strike a powerful blow against their assailants.”

While the second largest town in Montana has certainly had its share of media attention regarding sexual assaults, the disquieting fact running through Krakauer’s narrative is this: Missoula is typical.

Laura Pearson is a Chicago-based journalist specializing in arts and culture.

“Missoula”

By Jon Krakauer, Doubleday, 368 pages, $28.95