One obvious theme is Conrad's interest in the types of people who become involved in terrorism, described in the group of anarchists and revolutionaries who cluster around Verloc. In general, they are unsympathetic people who feel dispossessed of their heritage or suffer from frustrating mediocre lives. Verloc, the central figure in the group, is an example of a cynical man without political convictions who finds espionage and discussions of anarchy a useful way to make a living. The Professor is obsessed by a single idea; Ossipon is a predator who preys mainly on women, using political discussion and agitation as a mask. At the same time, Conrad avoids oversimplifying matters, for he shows that Verloc is indeed a pawn of a foreign power (he is given orders by an agent at the Russian embassy), and the British police, although well aware of the existence of fringe groups, find it pragmatic to allow them to exist because they can be useful scapegoats.

In short, scarcely any character connected with Verloc's group is actually innocent, except for Winnie Verloc's retarded brother, Stevie, and her crippled mother. Winnie Verloc herself, however, is less culpable than the men, although she finally loses her restraint and murders her stupid husband not because he tried to blow up the Greenwich Observatory, but because his scheming has led to the death of Stevie.

Another characteristically Conradian theme is a study of self-deception and its role in the development of moral corruption. Verloc is in many ways self-deceived, since he does not admit to himself how sordid his methods of making a living are, and he cannot acknowledge that he actually wanted to be rid of the mentally deficient Stevie. Similarly, Ossipon is not fully honest with himself about his tawdry way of preying on women. The Professor and some of the other anarchists are also self-deceiving about their political beliefs. The Professor, in particular, imagines himself to be strong and an enemy of the weak, yet he himself is a model of the socially impotent man seeking revenge on society through the fantasy of blowing it up. Through Inspector Heat and the higher English officials, Conrad also suggests that legal authority in Great Britain is tacitly complicit in the petty intrigues of the anarchists.

The extent to which people exploit other people is also a theme explored in The Secret Agent. Winnie allows herself to be sexually exploited by marrying Verloc, whom she does not love, for the sake of Stevie and her mother. Verloc also exploits his employers by his petty espionage, although they in turn are ready to use him without worrying about his fate. Ossipon lives by exploitation of women.

Contemporary readers may be disappointed with Conrad's treatment of terrorism, since they may believe that fictional terrorists should be portrayed in a more sinister light. However, Conrad seems to present his seedy band of terrorists as both potentially evil and banal in their enterprises. Indeed, a subtitle of the book might have been the title Hannah Arendt gave to her famous study of Adolph Eichmann—"The Banality of Evil."