The film comprises four parts, corresponding to the four parts of the novel. Some scenes are shown several times from different perspectives.
Briony Tallis is a 13-year-old girl from a wealthy English family, the youngest of three, and an aspiring writer. Her older sister Cecilia is educated at Cambridge University alongside Robbie Turner, the son of their housekeeper, whose school fees are paid by Cecilia's father. Though Robbie is headed for medical school soon, he is spending the summer gardening on the Tallis estate. The ginger-haired Lola Quince, age fifteen, and her younger twin brothers, Jackson and Pierrot, are cousins of Briony and Cecilia who are visiting the family amidst their parents' divorce. Lastly, Leon – Briony and Cecilia's brother – brings home a friend named Paul Marshall, who owns a chocolate factory that is acquiring a contract to produce army rations. The Tallis family is planning a special dinner, to which Leon happily invites Robbie, who accepts, much to Cecilia's annoyance.
Briony has just finished writing a play entitled The Trials of Arabella, which she describes being as about "the complications of love". Her cousins, however, are being unmanageable about staging the play, and she is considerably frustrated. Alone in her bedroom, she witnesses a significant moment of sexual tension between Robbie and her sister by the fountain, when her sister strips down to her underwear and dips into the fountain, to retrieve the lost part of a vase that Robbie has clumsily broken. Because Briony cannot hear what the two are saying, and has witnessed only a fraction of the scene, she misunderstands its dynamics, and the seed of her misplaced distrust in Robbie is sown.
Robbie writes several strained drafts of apology letters to Cecilia, including one, explicit and erotically-charged, that includes the word "cunt": In my dreams I kiss your cunt, your sweet wet cunt. He does not, however, intend to send it and, chuckling to himself, sets it to one side.
On his way to joining the Tallis family celebration, Robbie asks Briony to deliver his letter — only to realise too late that he has mistakenly given her the prurient one. Briony secretly reads the letter and becomes still more suspicious of Robbie's intentions, later convincing Lola that he is a "a sex maniac". She hands the letter, devoid of its envelope, to Cecilia, who is angry and embarrassed that she has read it.
That evening Briony encounters Cecilia and Robbie again, this time in the manqué seclusion of the library, where they are making love against a bookcase. The naïve Briony walks in to find them in the throes of sexual passion and falls under the misguided impression that Robbie is molesting her. At dinner, while Robbie and Cecilia secretly caress hands under the table, Briony is verbally aggressive toward Robbie but is cut short when her mother tells her to fetch the twins. Briony finds a note on their bed declaring that, in their anguish at their parents' divorce and unhappiness in their new lodgings, they have run off back home.
Immediately the family members split up in search of the twins on the large estate. As Briony goes off alone into the darkness to find them, she stumbles upon a man in a dinner suit raping Lola. On her arrival, the man dashes off into the darkness, and Briony runs to her cousin's aid. Lola, apparently traumatised, claims not to know the identity of her attacker — he covered her eyes —, but Briony is certain that it was Robbie.
Back at the estate, the police have been contacted. Briony insists that she "knows who did it". She tells everyone that it was Robbie, convinced due to the encounters between Robbie and Cecilia that she witnessed earlier in the day. In her testimony to the police, even though in reality she does not recall seeing the rapist's face, she claims that "I saw him; I saw him with my own eyes."
Finally, she shows the shocking letter to her mother, and now everyone believes her story — everyone, that is, except for Cecilia. "I wouldn't necessarily believe everything Briony tells you", she cautions her interviewers. "She's rather fanciful."
Robbie presently returns from his search, the twins safely in tow and wholly oblivious to the rape. He is arrested and sent to prison.
The story moves forward four and a half years, to the opening phases of the Second World War. Robbie, having been convicted but released from prison on condition that he enlist as a private in the British Expeditionary Force, is hiding in a French attic with two fellow soldiers cut off from their units during the German invasion of France. Although, as an ex-prisoner, he is not eligible to be a commissioned officer, his leadership skills and ability to speak French and read a map see him take the lead of his small group. The corporal, who formally outranks him, avoids confusion by addressing him as "guv".
Here the dénouement of the rape accusation is shown in dialogue and flashback. Before his deployment, Robbie was reunited with Cecilia in London, where they renewed their love and he made a promise to return to her. Like Cecilia, the eighteen-year-old Briony (now played by Romola Garai) has joined Cecilia's old nursing corps at St Thomas's in London (and thus given up her place at Cambridge) in an attempt to do "something practical" — although Cecilia accurately suspects that she is really trying to atone for her blunder, "the full extent of which," she has admitted in a letter, "I'm only now beginning to grasp." Her attempts at contacting her sister go unanswered: Cecilia has refused contact, blaming her for Robbie's imprisonment. It turns out, indeed, that Cecilia had broken off contact with all her family, since they all believe in Robbie's guilt.
Briony soon wins a reputation at the hospital for her mystique and reticence, with her fellow nurses gossiping about the chances of her having a secret fiancée. On being pressed on the matter by her closest companion Fiona, she denies the charge and claims further never to have been in love, although she does recall having had one crush: a flashback shows her deliberately jumping into a river in a bid to have Robbie save her. He duly obliges, and is furious. She remembers that, "as soon as I told him I loved him, the feeling sort of disappeared."
With his two companions, the wounded and very ill Robbie finally arrives at the beaches of Dunkirk, where he waits to be evacuated. After being told that all the soldiers are to leave the next day, he falls into a fitful sleep. Shortly thereafter, at the hospital at which she is a probationer nurse, Briony experiences the horror of the evacuation. In one scene, a mortally wounded French soldier (Jérémie Renier of L'Enfant) dies while she attempts to comfort him.
After seeing a newsreel depicting members of the Royal Family visiting Paul Marshall's chocolate factory, Briony attends the wedding of Marshall and her cousin Lola, and has a flashback of the night of the rape: as it turns out, it was Paul, not Robbie, whom she saw, with her own eyes, doing the deed. It is on this day that Briony summons up the courage to visit Cecilia's flat and apologise to her directly, recanting her accusation. Robbie, evacuated from Dunkirk, emerges from Cecilia's bedroom, awakened by the commotion of their argument, and angrily confronts Briony. Cecilia calms him, but the couple demand that Briony immediately tell her family and the authorities the truth, so that his name may be cleared. Robbie insists that she write to him precisely what happened, why she did it and give the details to asolicitor. Cecilia and Robbie appear long to have suspected that a certain servant boy, Danny Hardman, was the culprit, but Briony reveals that she knows it to be Paul Marshall, who, now married to Lola, cannot be implicated in a court of law by his wife. Briony takes the Underground away from her sister and Robbie, finally to tell the truth of the affair.
The film suddenly shifts forward to 1999, when an elderly Briony, interviewed on television (by Anthony Minghella) about her latest novel Atonement, is overcome with emotion and memory. She reveals that she is dying of vascula dementia, and that this novel will be her last, but that it is also her first, as she has been drafting it intermittently since her time at St Thomas's. Briony admits that the story is autobiographical and expresses great remorse at her actions. She admits that the end of the novel is, in fact, a fiction; in reality, both Robbie and Cecilia died before Briony could make amends, Robbie succumbing to septicemia the day before the evacuation at Dunkirk, and Cecilia perishing in the Ballham Tube Station flooding. Briony explains that she has altered the ending to give her sister and Robbie the chance at the happiness they both deserved, and which she took away from them. The film closes with a scene of a simple, seaside bliss between Cecilia and Robbie, together at long last. The scenery of the English cliff-side beach around them echoes that from a postcard that Cecilia gave Robbie on his departure for duty, as a promise that they would be together someday.
* It was hard to understand the movie if you havent read the novel or the synopsis of the movie beforehand. It's because the some scenes are not continuos, so viewer had to view the scene properly and understand that scene at the same time. Otherwise, you wouldn't understand what's the movie is all about. Anyway, I think the film is not bad.