The novel opens on a summer day in 1935 at the Tallis family's mansion in Surrey. Thirteen-year-old Briony has written a play in honor of the visit of her older brother Leon; guests include her three young cousins, refugees from their parent's breakup, Leon's friend Paul Marshall, the manufacturer of a chocolate bar called "Amo" that soldiers will be able to carry to war, and Robbie Turner, son of the family charlady. Jack Tallis is absent; he spends most of his time the War Ministry and with his mistress. His wife Emily is a semi-invalid. The elder daughter Cecilia is also present; she has just graduated from Cambridge and is at home for the summer. Rehearsals for Briony's play aren't going well, but Briony suddenly realizes that her destiny is to be a novelist. In the afternoon, Briony happens to be watching from a window when Cecilia strips off her clothes and plunges into the fountain on the lawn as Robbie looks on. Later Briony thinks she sees Robbie attacking Cecilia in the library, she reads a note meant for Cecilia, her cousin Lola is sexually assaulted, and she makes an accusation that she will repent for the rest of her life.
The next two parts of Atonement shift to the spring of 1940 as Hitler's forces are sweeping across the Low Countries and into France. Robbie Turner, wounded, joins the disastrous British retreat to Dunkirk. Briony has become a nurse in a military hospital. The fourth and final section takes place in 1999, as Briony celebrates her 77th birthday with the completion of a book about the events of 1935 and 1940, a novel called Atonement.