A lot happens in Atonement. And then some of it doesn't, which can get the plot even more tangled.
We start out at the Tallis family's very upper-class English home in 1935, a few years before World War II. The family is expecting a visit from their maternal cousins—the young twins Jackson and Pierrot, and 15-year-old Lola—all of whom have been temporarily cast adrift by their parents' divorce. The Tallis family is also expecting a visit from brother Leon and his friend, the chocolate magnate Paul Marshall. With five (count 'em, five) people arriving, the house is in something of an uproar—especially since father Jack Tallis is off in London at his government job, while mother Emily Tallis is largely incapacitated with a migraine.
In the middle of all this burble and bustle, Robbie Turner, the son of the housekeeper, realizes that he's fallen hopelessly, passionately in love with his childhood friend Cecilia Tallis. Their courtship rituals result—as these things will—in a series of awkward sexual displays. Cecilia jumps into a fountain in her underwear. Robbie accidentally gives Cecilia a letter he meant to destroy in which he tells her exactly what he wants to do with her. Then they do some of those things, not nearly privately enough, in the family library.
These embarrassing events are witnessed by Briony, Cecilia's imaginative 13-year-old sister. Spurred by confusion, and by her penchant for making up stories, she decides that Robbie is a "maniac" who is after her sister. This results in disaster when the twins run away after dinner, and everyone races out to search for them in the dark. Briony finds Lola, who has been sexually assaulted, and sees a figure running away into the darkness. Though she does not see his face, she is convinced that it was Robbie, and accuses him to the police. Robbie is taken to prison, despite the protests of Grace Turner (his mother) and Cecilia, who pledges her love and promises to wait for him.
The novel now jumps several years to 1940. Robbie has been released from prison to join the British Expeditionary Force (BEF) fighting in France against the Nazis. The war has gone horribly though, and so Robbie is trudging cross-country to the sea at Dunkirk, where he, his companions Mace and Nettle, and the rest of the British hope to be ferried across to England and safety. Robbie is wounded and increasingly delirious. He is sustained only by letters from Cecilia and his hopes for their future together. He finally collapses into sleep, waiting for the evacuation which is to begin the next day.
The narrative shifts to Briony. She is riddled with guilt since realizing that it wasn't Robbie who raped Lola. In part to try to atone for what she has done, she refuses to go study at Cambridge. Instead, to her mother's shock, she becomes a training nurse in London, where she cares for some of the first British soldiers wounded in the war.
On one of her days off from the hospital, Briony goes to visit her sister and offers to tell their parents and the court that her statement about Robbie was false. She discovers Robbie, who has survived the Dunkirk crossing, staying in her sister's apartment—scandal! (Or at least the landlady is scandalized, anyway.) Though it seems unlikely that Robbie's verdict can be overturned, she promises to retract her statement before an official witness, to tell their parents, and to write them a full account of what she did and why. She also tells them that Paul Marshall has married Lola, and that it was almost certainly he who raped her. Cecilia and Robbie do not forgive her, since she did ruin their lives and it's hard to get past that. But there is some sense of reconciliation.
The final part of the book is told by Briony in first person. She is old now, and a famous author. She has just learned that she has vascular dementia, a condition which will lead her to senility and then death in a couple of years. We learn that the book—yup, Atonement—is her novel, and that she is waiting to publish it until Lord and Lady Marshall—Paul and Lola—are dead and cannot sue. She recognizes that she will not outlive Lola, and that the book will therefore not be released in her lifetime. She also reveals that the book is not entirely truthful, and that Robbie and Cecilia did not reunite but instead died separately during the war. And if that doesn't make you cry when you turn the last page, then your heart is a big old lump of rock.