Set in London during the Blitz of World War II, the novel follows Arthur Rowe, a middle-aged man haunted by guilt over performing a mercy killing of his terminally ill wife. Tried for murder and briefly confined to an asylum, Rowe now lives alone in a bomb-damaged boarding house, isolated and self-loathing.
One afternoon, Rowe wanders into a charity fête for an organization called the Comforts for Mothers of the Free Nations. At the fortune-teller's booth, a woman named Mrs. Bellairs instructs him to guess a prize cake's weight as four pounds eight and a half ounces. He does and wins, but the organizers pressure him to return the cake. Rowe refuses and takes it home, where his landlady weighs it at under three pounds, proving the winning weight was fraudulent.
That evening, a small, dark stranger with shoulders twisted by infantile paralysis (polio) moves into the boarding house and visits Rowe during an air raid. He claims he has been sent to retrieve the cake and crumbles each slice as if searching for something inside. Rowe detects hyoscine in his tea, the same sedative he used to kill his wife. A bomb destroys the house before Rowe can act. The stranger is found injured; the cake is largely destroyed.
Determined to learn who tried to poison him, Rowe hires a private detective named Mr. Rennit, who assigns his agent Jones to shadow Rowe. Rowe visits the charity's office, where he meets Anna Hilfe, a pretty Austrian refugee, and her brother Willi Hilfe, a charming young man eager to investigate. They obtain Mrs. Bellairs's address, and Willi accompanies Rowe to a séance at her house on Park Crescent. The group includes Dr. Forester, an elderly doctor with a noble face, and Cost, a City businessman—both covert members of the spy ring. Anna phones to warn Rowe to leave, but before he can escape, the lights go out. When they return, Cost lies dead, stabbed with Rowe's own knife, stolen from his pocket. Willi helps Rowe escape through a window, urging him to go underground.
Rowe hides in public shelters but finds no mention of the murder in the papers. Rennit has reported him to the police. Penniless, Rowe is manipulated by an elderly bookseller into carrying a suitcase to a room at the Regal Court hotel, where he finds Anna. She tells him the room is a trap: The phone is dead, the lights are cut, and the exits are watched. As air-raid sirens sound, Rowe opens the suitcase, and the narrative cuts away.
Book Two opens months later at a country nursing home. A patient called Richard Digby is revealed to be Rowe, entirely without memory of his adult life. Tended by Johns, an earnest assistant who reveres the clinic's director, Dr. Forester, Digby is happy in his amnesia, freed from guilt and responsibility. Anna visits and tells him they were friends, that he saved her life in a bombing, and that he is not married. Over subsequent visits they acknowledge deeper feelings, and she urges him not to recover his memory, wishing he could remain innocent and unburdened. Through newspapers and conversations with Johns, Digby learns about a Nazi practice called the "Ministry of Fear," in which agents blackmail prominent people by exploiting their secrets. He also discovers that military documents were twice reported missing.
Troubling signs emerge. Major Stone, another patient, insists enemies are digging on an island in the grounds' pond. Poole, a small attendant from the sick bay, unsettles Digby with an unplaceable flash of recognition; the reader recognizes Poole as the stranger who poisoned Rowe's tea. Dr. Forester restricts Digby's freedoms, forbidding newspapers and Anna's visits. When Forester leaves one evening, Digby sneaks into the sick bay and finds Stone bound in a straitjacket. Forester returns and confronts Digby, thrusting a newspaper photograph at him and calling the man pictured a murderer. Digby compares his bearded face with the clean-shaven photo and recognizes himself as Arthur Rowe. His memories begin flooding back. He resolves to endure the truth rather than destroy himself as a previous patient did.
Rowe escapes to London and presents himself at Scotland Yard, where intelligence officer Mr. Prentice reveals the conspiracy. Cost is alive; the séance murder was staged to frame Rowe and force him underground. Secret military documents were stolen and photographed, and the film was hidden in the cake, to be collected by an agent using the correct weight as a password. Mrs. Bellairs mistakenly gave the weight to Rowe. Prentice takes Rowe to a tailor's shop where Cost works under the name Ford. Discovered, Cost makes a final phone call and kills himself with cutting shears. Rowe catches most of the number Cost dialed but misses the final digit.
Prentice raids Mrs. Bellairs's house and then drives to the nursing home. There, Johns has shot both Forester and Poole, unable to bear complicity in Forester's plan to murder Stone. Stone is found dead in the sick bay, asphyxiated with chloroform. On the island, police unearth the remains of Jones, the private detective, murdered and buried there months ago. The film negative is not found.
Back in London, Rowe withholds the partial phone number from Prentice and systematically dials possible combinations from a phone box. When he reaches the final possibilities, he hears Anna's voice and hangs up, devastated.
Rowe goes to Anna's flat in Battersea. She confesses that Willi is the organizer of the spy ring. He staged Cost's fake murder, arranged the bombing at the Regal Court to kill both Rowe and Anna for her betrayal, and kept Rowe hidden at the clinic after the explosion. Anna watched Rowe there as part of her assignment but genuinely fell in love with him and tried to delay his memory's return. Willi possesses the film negative and plans to escape to Ireland on the 7:20 train from Paddington.
Anna breaks Willi's wrist with a brass candlestick and takes his gun, then locks Rowe out to negotiate alone with her brother. She emerges with what she says are the photographs, but Rowe recognizes them as prints, not the negative. Willi has escaped to Paddington; Anna let him go out of family loyalty.
During an air raid, Rowe finds Willi on the train and takes him off. In the station lavatory, Rowe cuts open the padded shoulder of Willi's jacket and finds the film negative. Willi begs for the gun, saying he would rather shoot himself than face interrogation. When Rowe refuses, Willi reveals Rowe's past as revenge: Rowe poisoned his wife, was tried for murder, and was sent to an asylum. Rowe's full memory returns. He understands what Anna was protecting him from: not just danger, but the return of unbearable guilt.
Moved by pity and the recognition that Willi is doomed, Rowe returns the gun. Willi retreats to a cubicle and shoots himself. Rowe walks back to Anna's flat, now possessing all his memories. He lies to her, saying Willi died immediately without revealing anything about Rowe's past. They sit together, pledged to a future of mutual guardedness: She tries to shield him from his past, and he conceals that he already knows it.