The Secret Agent, set in London in 1886, follows the life of Mr. Verloc and his job as a spy. Verloc is also a businessman who owns a shop which sells pornographic material, contraceptives, and bric-a-brac.

Verloc's friends are a group of anarchists. Although largely ineffectual as terrorists, their actions are known to the police. While a member of an anarchist cell, Verloc is also secretly employed as an agent provocateur. His service history shows that 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.

The novel deals broadly with the notions of anarchism, espionage, and terrorism. It portrays anarchist or revolutionary groups before many of the social uprisings of the twentieth century.

Because of its terrorist theme, The Secret Agent was noted as "one of the three works of literature most cited in the American media" around two weeks after 11 September 2001. The Secret Agent was ranked amongst the best novels of the 20th century.