Ludlum has said that he writes from a sense of outrage, often at the abuse of power by political extremists of right and left. The Holcroft Covenant evinces the theme of abuse of government power, where an arch-right terrorist organization makes free use of government services to the detriment of a good citizen, Noel Holcroft, who in this way represents the average citizenry. Almost a paranoid quality rises from this spy thriller, where for half the novel, at least, the forces of evil seem to have free, unlimited access to the computer banks, phone networks, surveillance police and other potentially coercive apparatus of the modern state, while the hero is comparatively isolated and must fend for himself.

A complementary theme arises from this unfair conflict, and it is the central theme of the novel: the ability of the individual to struggle, sometimes successfully, against the collective enemy, or even the whole coercive state. As The Holcroft Covenant progresses, Noel Holcroft becomes more adept at the deadly maneuvers of intrigue, violence and manipulation that his adversaries use against him, and in the end he is well on the way to winning.

Still a third theme, closely related to the other two, is implicit in this novel. The Holcroft Covenant reemphasizes the age old theme of the deceptiveness of evil. For much of the book, Holcroft is misled by evil forces posing as good, and he mistakes good and evil forces repeatedly until the final unveilings near the end of the book. Such deliberate confusions are part and parcel of any suspense or mystery story, but the degree to which deceptiveness comes into play raises this concern to the thematic level. Ludlum is also basically optimistic in his depiction of this theme of deceptive evil, since Holcroft is able to sort truth from lies, good from evil, when really put to the test.