Briony Tallis is a literary, self-important 13-year-old who lives in an English country estate in 1935. Her cousins, 15-year-old Lola Quincey and 9-year-old twins Jackson and Pierrot Quincey, are coming to stay with the Tallises because their parents are embroiled in a divorce. Meanwhile, Briony’s older sister Cecilia holds unresolved romantic feelings for Robbie Turner, the Tallises’ gardener (Robbie’s romantic feelings for Cecilia, meanwhile, are passionately resolved). Thanks to the Tallises’ funding, Robbie studies with Cecilia at Cambridge and plans to become a doctor. From a window of the estate, Briony witnesses the two of them accidentally break a family heirloom vase in front of a fountain. When Cecilia removes her clothes in front of Robbie to retrieve the shards from the fountain, Briony starts to think Robbie is a threat to her sister. Later, Robbie gives Briony a letter of apology to give to Cecilia, but accidentally hands her a vulgar draft instead. Briony reads the letter and becomes convinced Robbie is a menace. When Robbie realizes his error, he goes to Cecilia to apologize. This apology turns to passionate lovemaking in the family library. Briony enters the room and interrupts, further cementing her resentment and suspicion of Robbie.
The family gathers for a dinner to commemorate the visit of Leon, the oldest Tallis child. He has brought a friend, Paul Marshall, with him. Paul is the heir to a chocolate fortune. The twins leave the dinner table, and leave a letter behind explaining they have run away from the house because they miss their parents. The guests assemble search parties to look for the boys on the grounds.
Briony, searching alone, finds Lola being raped in a remote part of the estate. The assailant runs away before Briony can identify him, but as she consoles Lola she convinces both Lola and herself that she saw Robbie commit the crime. Briony leads Lola back to the house and delivers her story to all the adults present. Policemen arrive and Briony testifies that she saw Robbie commit the crime. After many hours, Robbie returns to the house with the twins; he had been searching for them alone all night. When he gets back, he is taken into police custody.
Part Two resumes after Robbie has served three and a half years in prison for Lola’s assault. During that time, he has been in constant correspondence with Cecilia, even though she has not been allowed to visit him in person. She has cut ties with her family and started a career as a nurse. Cecilia’s latest letter informs Robbie that Briony has contacted her in the hopes of retracting the false testimony she made years earlier.
The outbreak of World War II allows Robbie to end his sentence by enlisting in the army. He goes to fight in France. When Part Two begins, he must walk to the coast with his comrades Corporal Nettle and Corporal Mace in order to evacuate with the British forces. During this walk, the men behold disturbing carnage. Despite having a painful shrapnel wound, Robbie makes it to the coast and is evacuated.
Part Three focuses on Briony, who has foregone college to work as a nurse during the war. Work is demanding, and she is intimidated by her overseer, Nurse Drummond. An influx of injured men from the French evacuation arrives to the hospital, and the harrowing experience of treating them causes Briony to mature. In her rare free time, Briony writes stories, which she submits to magazines unsuccessfully.
A letter from her father informs Briony that Paul and Lola are to be married. She attends their wedding and, afterwards, pays a visit to Cecilia. Unexpectedly, Robbie is present as well. The atmosphere is tense, but Briony agrees to take the steps necessary to alert her family and the relevant legal authorities of her change in testimony. Cecilia and Robbie see Briony off, and Briony understands that after she finishes the tasks she agreed to, she must begin an in-depth process of “atonement.”
The book’s epilogue reveals that this atonement process was to write the preceding novel itself. Briony, now 77, narrates in the first person. She has just been diagnosed with irreversible dementia. She describes going to a library to donate her correspondence with Corporal Nettle—used to write this book—and afterwards attends a birthday party thrown by her surviving relatives, including Pierrot and Leon. While Briony longs to publish her memoir, she cannot do so while Paul and Lola remain alive. They are now well-connected socialites and will doubtless sue her for libel. Briony admits that her novelization has changed some details—for example, Robbie and Cecilia both actually perished in the war, but her fiction allowed them to live—but she reflects that even though achieving atonement will be impossible for her, her attempt to do so is indispensable.