The Secret Agent follows the exploits of Mr. Veloc, a secret agent who spies on revolutionary groups for an unspecified Embassy. The Embassy, hoping to incite public outrage about anarchists, orders Veloc to blow up an Observatory. Veloc carries out his orders, but his mentally impaired brother-in-law Stevie is killed in the blast. When Veolc's wife Winnie discover's her husband's role in her brother's death, she kills him. This novel of intrigue explores themes of terrorism, anarchism, and exploitation.
The novel is set in London in 1886 and follows the life of Mr. Verloc, a secret agent. Verloc is also a businessman who owns a shop which sells pornographic material, contraceptives, and bric-a-brac. He lives with his wife Winnie, his mother-in-law, and his brother-in-law, Stevie. Stevie has a mental disability, possibly autism, which causes him to be very excitable; his sister, Verloc's wife, attends to him, treating him more as a son than as a brother. Verloc's friends are a group of anarchists of which Comrade Ossipon, Michaelis, and "The Professor" are the most prominent. Although largely ineffectual as terrorists, their actions are known to the police. The group produce anarchist literature in the form of pamphlets entitled F.P. , an acronym for The Future of the Proletariat .
The novel begins in Verloc's home, as he and his wife discuss the trivialities of everyday life, which introduces the reader to Verloc's family. Soon after, Verloc leaves to meet Mr. Vladimir, the new First Secretary in the embassy of a foreign country. Although a member of an anarchist cell, Verloc is also secretly employed by the Embassy as an agent provocateur. Vladimir informs Verloc that from reviewing his service history he is far from an exemplary model of a secret agent and, to redeem himself, must carry out an operation– the destruction of Greenwich Observatory by a bomb explosion. Vladimir explains that Britain's lax attitude to anarchism endangers his own country, and he reasons that an attack on 'science', which he claims is the current vogue amongst the public, will provide the necessary outrage for suppression. Verloc later meets with his friends, who discuss politics and law, and the notion of a communist revolution. Unbeknownst to the group, Stevie, Verloc's brother-in-law, overhears the conversation, which greatly disturbs him.
The novel flashes forward to after the bombing has taken place. Comrade Ossipon meets The Professor, who discusses having given explosives to Verloc. The Professor then describes the nature of the bomb which he carries in his coat at all times: it allows him to press a button which will blow him up in twenty seconds, and those nearest to him. After The Professor leaves the meeting, he stumbles into Chief Inspector Heat. Heat is a policeman who is working on the case regarding a recent explosion at Greenwich, where one man was killed. Heat informs The Professor that he is not a suspect in the case, but that he is being monitored due to his terrorist inclinations and anarchist background. Knowing that Michaelis has recently moved to the countryside to write a book, the Chief Inspector informs the Assistant Commissioner that he has a contact, Verloc, who may be able to assist in the case. The Assistant Commissioner shares some of the same high society acquaintances with Michaelis and is chiefly motivated by finding the extent of Michaelis's involvement in order to assess any possible embarrassment to his connections. He later speaks to his superior, Sir Ethelred, about his intentions to solve the case alone, rather than rely on the effort of Chief Inspector Heat.
The novel then flashes back to before the explosion, taking the perspective of Winnie Verloc and her mother. At home, Mrs. Verloc's mother informs the family that she intends to move out of the house. Mrs. Verloc's mother and Stevie use a hansom which is driven by a man with a hook in the place of his hand. The journey greatly upsets Stevie, as the driver's tales of hardship coupled with his menacing hook scare him to the point where Mrs. Verloc must calm him down. On Verloc's return from a business trip to the continent, his wife tells him of the high regard that Stevie has for him and she implores her husband to spend more time with Stevie. Verloc eventually agrees to go for a walk with Stevie. After this walk, Mrs. Verloc notes that her husband's relationship with her brother has improved. Verloc then tells his wife that he has taken Stevie to go and visit Michaelis, and that Stevie would stay with him in the countryside for a few days.
As Verloc is talking to his wife about the possibility of emigrating to the continent, he is paid a visit by the Assistant Commissioner. Shortly thereafter, Chief Inspector Heat arrives to speak with Verloc, without knowing that the Assistant Commissioner had left with Verloc earlier that evening. The Chief Inspector tells Mrs. Verloc that he had recovered an overcoat at the scene of the bombing which had the shop's address written on a label. Mrs. Verloc confirms that it was Stevie's overcoat, and that she had written the address. On Verloc's return, he realises that his wife knows her brother has been killed by Verloc's bomb, and confesses what truly happened. A stunned Mrs. Verloc, in her anguish, then fatally stabs her husband.
After the murder, Mrs. Verloc flees her home, where she chances upon Comrade Ossipon, and begs him to help her. Ossipon assists her while confessing romantic feelings but secretly with a view to possess Mr Verloc's bank account savings. They plan to run away and he aids her in taking a boat to the continent. However, her instability and the revelation of Mr. Verloc's murder increasingly worry him, and he abandons her, taking Mr Verloc's savings with him. He later discovers in a newspaper that a woman had disappeared, leaving behind her a wedding ring, before drowning herself in the English Channel.