Set in America in 1951, the second year of the Korean War, Indignation is narrated by Marcus Messner, a college student from New Jersey, who describes his sophomore year at Winesburg College in Ohio. Marcus transfers to Winesburg from Robert Treat College to escape his father, a butcher, who appears to have become consumed with fear about the dangers of adult life, the world, and the uncertainty that awaits his son.
At Winesburg College, Marcus becomes infatuated with a fellow student, Olivia Hutton, a survivor of a suicide attempt. The sexually inexperienced Marcus is bewildered when Olivia performs fellatio on him during their one and only date... Marcus' mother objects to his dating someone who attempted suicide and makes him vow to end their relationship.
Marcus has an adversarial relationship with the dean of men, Hawes Caudwell. In a meeting in Dean Caudwell's office, Marcus objects to the chapel attendance requirement on the grounds that he is an atheist. In this meeting, he quotes extensively from Bertrand Russell's essay "Why I Am Not a Christian". Later, the dean finds Marcus guilty of hiring another student to attend chapel in his place; when Marcus refuses to attend double the amount of chapel services as punishment, the dean expels him. His expulsion allows the U.S. Army to draft him and send him to fight in Korea where he is killed. Early in the novel, Marcus explains that he is dead and telling his story from the afterlife; later it is revealed that he is unconscious from his combat wounds and the morphine that has been administered.