William Stoner is born on a small farm in 1891. One day his father suggests he should attend the University of Missouri to study agriculture. Stoner agrees but, while studying a compulsory literature course, he quickly falls in love with literary studies. Without telling his parents, Stoner quits the agriculture program and studies humanities. He completes his MA in English and begins teaching. In graduate school, he befriends fellow students Gordon Finch and Dave Masters. World War I begins, and Gordon and Dave enlist, but despite pressure from Gordon, Stoner remains in school. Masters is killed in France, while Finch sees action and becomes an officer. At a faculty party, Stoner meets and becomes infatuated with a young woman named Edith. He woos her and she marries him.
Stoner’s marriage to Edith is bad from the start and it becomes clear that Edith has profound emotional problems, and is bitter because she cancelled a trip to Europe to marry Stoner. After three years of marriage, Edith suddenly informs Stoner that she wants a baby, becomes passionately sexual for a brief period, but after their daughter Grace is born, she remains bedridden for nearly a year. Stoner largely cares for their child alone. He grows close to her: she spends most of her time with him in his study. Stoner gradually realizes that Edith is waging a campaign to separate him from his daughter emotionally. For the most part, Stoner accepts Edith's mistreatment. He begins to teach with more enthusiasm, but still, year in and year out, his marriage with Edith remains perpetually unsatisfactory and fraught. Grace becomes an unhappy, secretive child who smiles and laughs often but is emotionally hollow.
At the University, Finch becomes the acting dean. Stoner feels compelled by his conscience to fail a student named Charles Walker, a close protégé of a colleague, Professor Hollis Lomax. The student is clearly dishonest and cannot fulfil the requirements of Stoner's course but, despite this, the decision to expel or retain Walker is put on hold. After his promotion to head of the department, Lomax takes every opportunity to exact revenge upon Stoner throughout the rest of his career. A collaboration between Stoner and a younger instructor in the department, Katherine Driscoll, develops into a romantic love affair. Ironically, after the affair begins, Stoner’s relationships with Edith and Grace also improve. Edith finds out about the affair, but does not seem to mind. When Lomax learns about it, however, he begins to put pressure on Katherine, who also teaches in the English department. Stoner and Driscoll agree it best to end the affair so as not to derail the academic work they both feel called to follow. Katherine quietly slips out of town, never to be seen by him again.
Eventually, Stoner, older now and hard of hearing, is becoming a legendary figure in the English department despite Lomax's opposition. He begins to spend more time at home, ignoring Edith's signs of displeasure at his presence. Entering adulthood, Grace enrolls at the University of Missouri. The following year, Grace announces she is pregnant and marries the father of her child--but he enlists in the army and dies before the baby is born. Grace goes to St. Louis with the baby to live with her husband's parents. She visits Stoner and Edith occasionally, and Stoner realizes that Grace has developed a drinking problem.
As Stoner’s life is coming to an end, his daughter Grace comes to visit him. Deeply unhappy and addicted to alcohol, Grace halfheartedly tries to reconcile with Stoner, and he sees that his daughter, like her mother, will never be happy. When Grace leaves, Stoner feels as though the young child that he loved died long ago. Stoner thinks back over his life. He thinks about where he failed, and wonders if he could have been more loving to Edith, if he could have been stronger, or if he could have helped her more. Later, he believes that he is wrong to think of himself as a failure. During an afternoon when he is alone, he sees various young students passing by on their way to class outside his window, and he dies, dropping his copy of the one book that he published years earlier as a young professor.
