Missoula begins with the story of Allison Huguet, a young woman from Missoula, Montana who is raped by Beau Donaldson, a member of the University of Montana football team. In the process of telling Allison’s story, John Krakauer gives key background information on the city of Missoula. He describes the importance of football to the local culture and the privileges given to football players in the town. Beau and Allison are long time family friends who consider each other like brother and sister. In September of 2010, after a night of heavy drinking and partying at Beau’s house, Allison wakes up to find Beau raping her. Allison goes to the hospital to have a rape kit collected. The next day, her trauma is reawakened when she sees Beau on the sidelines of a UM football game. Allison’s friend, Keely Williams, supports her and convinces her to see if she can get Beau to admit to his crime. Beau does, and Allison struggles with whether or not she should report him to the police. After fifteen months, Allison decides reporting Beau is the only way to get him to take full responsibility for his actions.
Allison is close with a detective at the Missoula Police Department, Detective Guy Baker. Detective Baker works hard to collect evidence for Allison’s case. By securing a warrant to tape-record Beau without his knowledge, Allison and Detective Baker get Beau to confess his crime over the phone. Allison’s story is, in some ways, exceptional. The police take her claim seriously. After Beau’s confession, Krakauer describes the rapes of several other women and how Missoula law enforcement officials disrespect them and dismiss their claims. Kerry Barrett is sexually assaulted in a man’s apartment. Calvin Smith rapes Kaitlyn Kelly in her dorm room, and Kelsey Belnap is gang raped by four members of the University of Montana football team. The police do little to gather evidence for their claims, and public prosecutors in the Missoula County Attorney’s Office decide that there is insufficient probable cause to prosecute their rapes in court.
Despite having her claim dismissed by the city of Missoula, Kaitlyn Kelly reports her rape to the University of Montana. Using a new standard of evidence in which it must only prove that it is “more likely than not” that a rape was committed, the University expels Calvin Smith. At Smith’s University Court hearing, public prosecutor Kirsten Pabst testifies on Smith’s behalf. Pabst explains why she dismissed the charges against Smith. The University Court finds Smith guilty, and Kelly is shocked that Pabst, the woman responsible for prosecuting rape cases in Missoula County, would testify on behalf of her rapist. Articles begin to appear in the Missoulian, the local newspaper, describing rapes on campus. The articles question the way the rapes are being handled by police and prosecutors. Then, the news breaks that “Cecilia Washburn” (a pseudonym that Krakauer uses for the woman throughout the book) has been raped by the star quarterback of the UM football team, Jordan Johnson. Krakauer recounts the details of Cecilia Washburn’s rape. Jordan Johnson is found guilty of violating the student conduct code, and with the help of his lawyer, David Paoli, he appeals the University of Montana’s ruling four times. Finally, the charge against Johnson is dismissed.
Then Krakauer resumes the story of Allison and Beau Donaldson. Allison fights with public prosecutor Shaun Donovan, urging him to offer a maximum sentence that will require Beau to serve time in the state prison. Allison and her family meet with County Attorney Fred Van Valkenberg to complain of the way Donovan is handling Allison’s case against Beau. They are worried he will not argue convincingly for the maximum sentence, thirty years in the state prison with twenty years suspended. Responding to mounting pressure from the media and an ongoing investigation by the U.S. Department of Justice into the way rape is being handled in Missoula, Fred Van Valkenberg agrees to argue Allison’s case. At the hearing, Beau’s witnesses find it difficult to argue that he should not be punished, and the judge gives Beau the maximum sentence, thirty years in the state prison with twenty years suspended. Beau must serve two and a half years before he is eligible for parole.
Kirsten Pabst retires from the Missoula County Attorney’s Office and enters private practice. She joins David Paoli to defend Jordan Johnson in court. In the wake of Beau’s conviction, Pabst and Paoli argue that it will be impossible for Johnson to get a fair trial. Their motions to dismiss Johnson’s case are rejected, however, and Johnson’s trial begins in February of 2013. Paoli and Pabst turn the courtroom into a stage for a theatrical performance of Jordan Johnson’s defense. They make every possible argument that might defend Johnson. In the process, they smear Cecilia Washburn’s reputation. The jury finds Johnson not guilty.
After Johnson’s trial, the U.S. Department of Justice (DOJ) concludes its investigation into rape in Missoula. It issues recommendations for the Missoula County Attorney’s Office. The DOJ recommendations require the office to hire independent investigators for rape cases and to staff victim advocates. County Attorney Fred Van Valkenberg launches a lawsuit against the DOJ claiming its mandatory recommendations are a violation of local authority. In the end, Van Valkenberg steps down as County Attorney and abandons the lawsuit. Kirsten Pabst, who, earlier, failed to prosecute rape cases, testified on behalf of a rapist in University Court, and gained fame in Missoula for successfully defending Jordan Johnson in criminal court, runs for Missoula County Attorney. She campaigns on the promise that she will make the office harder on alleged rapists and more compassionate to rape victims. Pabst is elected and takes office on January 1, 2015.