Darkness at Noon is divided into four parts: The First Hearing, the Second Hearing, the Third Hearing, and the Grammatical Fiction.
The novel begins with Rubashov's arrest in the middle of the night by two men from the secret police (in the USSR, it was called the NKVD). When they came for Rubashov, they woke him from a dream in which he was being arrested by the Gestapo. One of the men is about Rubashov's age, the other is somewhat younger. The older man is formal and courteous, the younger is brutal. The difference between them introduces the first major theme of Darkness at Noon : the passing of the older, civilised generation, and the barbarism of their successors.
Imprisoned, Rubashov is at first relieved to be finished with the anxiety of dread during mass arrests. He is expecting to be kept in solitary confinement until he is shot. He begins to communicate with No. 402, the man in the adjacent cell, by using a tap code. Rubashov quickly realises that they don't have much to discuss. Unlike Rubashov, No. 402 is not an intellectual; he just wants to hear the details of Rubashov's latest sexual encounter. Rubashov humours him for a time, but is too embarrassed to continue.
He thinks of the Old Bolsheviks, No. 1, and the Marxist interpretation of history. Throughout the novel Rubashov, Ivanov, and Gletkin speculate about historical processes and how individuals and groups are affected by them. Each hopes that, no matter how vile his actions may seem to their contemporaries, history will eventually absolve them. This is the faith that makes the abuses of the regime tolerable as the men consider the suffering of a few thousand, or a few million people against the happiness of future generations. They believe that gaining the socialist utopia, which they believe is possible, will cause the imposed suffering to be forgiven.
Rubashov meditates on his life: since joining the Party as a teenager, Rubashov has officered soldiers in the field, won a commendation for "fearlessness", repeatedly volunteered for hazardous assignments, endured torture, betrayed other communists who deviated from the Party line, and proven that he is loyal to its policies and goals. Recently he has had doubts. Despite 20 years of power, in which the government caused the deliberate deaths and executions of millions, the Party does not seem to be any closer to achieving the goal of a socialist utopia. That vision seems to be receding. Rubashov is at a quandary, between a lifetime of devotion to the Party, and his conscience and the increasing evidence of his own experience on the other.
From this point, the narrative switches back and forth between his current life as a political prisoner and his past life as one of the Party elite. He recalls his first visit to Berlin about 1933, after Hitler gained power. Rubashov was to purge and reorganise the German Communists. He met with Richard, a young German Communist cell leader who had distributed material contrary to the Party line. In a museum, underneath a picture of the Pieta, Rubashov explains to Richard that he has violated Party discipline, become "objectively harmful", and must be expelled from the Party. A Gestapo man hovers in the background with his girlfriend on his arm. Too late, Richard realises that Rubashov has betrayed him to the secret police. He begs Rubashov not to "throw him to the wolves," but Rubashov leaves him quickly. Getting into a taxicab, he realises that the taxicab driver is also a communist. The taxicab driver offers to give him free fare, but Rubashov pays the fare. As he travels by train, he dreams that Richard and the taxicab driver are trying to run him over with a train.
This scene introduces the second and third major themes of Darkness at Noon . The second, suggested repeatedly by the Pieta and other Christian imagery, is the contrast between the brutality and modernity of Communism on the one hand, and the gentleness, simplicity, and tradition of Christianity. Although Koestler is not suggesting a return to Christian faith, he implies that Communism is the worse of the two alternatives.
The third theme is the contrast between the trust of the rank and file communists, and the ruthlessness of the Party elite. The rank and file trust and admire men like Rubashov, but the elite betrays and uses them with little thought. As Rubashov confronts the immorality of his actions as a party chief, his abscessed tooth begins to bother him, sometimes reducing him to immobility.
Rubashov recalls being arrested soon after by the Gestapo and imprisoned for two years. Although repeatedly tortured, he never breaks down. After the Nazis finally release him, he returns to his country to receive a hero's welcome. No. 1's increasing power makes him uncomfortable but he does not act in opposition; he requests a foreign assignment. No. 1 is suspicious but grants the request. Rubashov is sent to Belgium to enforce Party discipline among the dock workers. After the Italian invasion of Ethiopia in 1935, the League of Nations and the Party condemned Italy and imposed an international embargo on strategic resources, especially oil, which the Italians needed. The Belgian dock workers are determined not to allow any shipments for Italy to pass through their port. As his government intends to supply the Italians with oil and other resources secretly, Rubashov must convince the dock workers that, despite the official policy, as Communists they must unload the materials and send them to the Italians.
Their cell leader, a German communist immigrant nicknamed Little Loewy, tells Rubashov his life's story. He is a communist who has sacrificed much for the Party, but is still completely dedicated. When all the workers have gathered, Rubashov explains the situation. They react with disgust and refuse his instructions. Several days later, Party publications denounce the entire cell by name, virtually guaranteeing arrest by the Belgian authorities, who were trying to suppress Communism. Little Loewy hangs himself. Rubashov then begins a new assignment.
In the novel, after about a week in prison, he is brought in for the first examination or hearing, which is conducted by Ivanov, an old friend. Also a veteran of the Civil War, he is an Old Bolshevik who shares Rubashov's opinion of the Revolution. Rubashov had then convinced Ivanov not to commit suicide after his leg was amputated due to war wounds. Ivanov says that if he can persuade Rubashov to confess to the charges, he will have repaid his debt. With confession, Rubashov can lessen his sentence, to 5 or 10 years in a labour camp, instead of execution. He simply has to co-operate. The charges are hardly discussed, as both men understand they are not relevant. Rubashov says that he is "tired" and doesn't "want to play this kind of game anymore." Ivanov sends him back to his cell, asking him to think about it. Ivanov implies that Rubashov can perhaps live to see the socialist utopia they've both worked so hard to create.
The next section of the book begins with an entry in Rubashov's diary; he struggles to find his place and that of the other Old Bolsheviks, within the Marxist interpretation of history.
Ivanov and a junior examiner, Gletkin, discuss Rubashov's fate in the prison canteen. Gletkin urges using harsh, physical methods to demoralise the prisoner and force his confession, while Ivanov insists that Rubashov will confess after realising it is the only "logical" thing to do, given his situation. Gletkin recalls that, during the collectivisation of the peasants, they could not be persuaded to surrender their individual crops until they were tortured (and killed). Since that helped enable the ultimate goal of a socialist utopia, it was both the logical and the virtuous thing to do. Ivanov is disgusted but cannot refute Gletkin's reasoning. Ivanov believes in taking harsh actions to achieve the goal, but he is troubled by the suffering he causes. Gletkin says the older man must not believe in the coming utopia. He characterises Ivanov as a cynic and claims to be an idealist.
Their conversation continues the theme of the new generation taking power over the old: Ivanov is portrayed as intellectual, ironical, and at bottom humane, while Gletkin is unsophisticated, straightforward, and unconcerned with others' suffering. Ivanov has not been convinced by the younger man's arguments. Rubashov continues in solitary.
Taking over the interrogation of Rubashov, Gletkin uses physical abuses, such as sleep deprivation and forcing Rubashov to sit under a glaring lamp for hours on end, to wear him down. Rubashov finally capitulates.
As he confesses to the false charges, Rubashov thinks of the many times he betrayed agents in the past: Richard, the young German; Little Loewy in Belgium, and Arlova, his secretary-mistress. He recognises that he is being treated with the same ruthlessness. His commitment to following his logic to its final conclusion—and his own lingering dedication to the Party—cause him to confess fully and publicly.
The final section of the novel begins with a four-line quotation ("Show us not the aim without the way ...") by the German socialist Ferdinand Lasalle. The novel ends with Rubashov's execution.