Old Bolsheviks vs. New Generation
When Rubashov is arrested, the older of the two Secret Policeme is courteous and civil; there is still an air of propriety about him He is not brutal; by contrast, the younger of the two is brutal, rude, and uncouth. This difference introduces the theme of the difference between Old Bolsheviks, such as Rubashov, and new Communists, who want to get rid of their predecessors and are brutal in doing so.
Rubashov also worries about the way in which he and his colleagues will be seen in the context of history through the eyes of the younger generation. He hopes that although some of his actions have been disgusting and depraved, they will be viewed as necessary and that he will receive some kind of historical absolution from them. The matter concerns him greatly because at the end of the day he does not trust the younger generation to have the intelligence to view his actions correctly or intellectually.
The Promise of a Utopian Society
The Soviet government consistently promised a Utopian society, and held it out as a carrot on a stick for all of its citizens but particularly those who were cogs in the wheel of the Soviet machine. Rubashov himself was one of these cogs. By promising that the atrocities that are being committed are for the benefit of future generations, for whom they are creating a near-perfect society, the regime are effectively weighing the abuses done to a few thousand against a benefit for millions in generations to come. This minimises what is being done in their name, without anything ever improving for the present generation.
Naive Beliefs of Party Members
The "rank and file" of the party are not terrifically smart people; if they were they would not blindly follow the leaders of the regime in the way that they do. The "elite" are ruthless and brutal but do not really share this with the members. Rank and file members admire Rubashov and men like him, and they trust him as well. The party elite use him for their own agenda and purpose and promptly betray and execute him when he has outlived his usefulness. The ordinary party members do not realize this and hold the elite up as heroes of the Communist party.
Gentility of Christianity
The theme of Christianity being preferable to Communism is not one that is addressed by the characters in the novel, but by the author of it. Koestler compares the gentleness and mercy of Christianity with the brutality and complication of Communism. He does not want either to exist at the expense of the other, but believes that a return to Christianity would make the Communists more merciful, and would prevent them from conducting mass executions in the name of something meaningful. Christianity brings with it a tradition that connects people with their ancestors in a positive way, which is also a positive and in many ways would take away the party's ability to get rid of people without any explanation whatsoever.
Similarity Between Dictatorships
Communists and Fascists consider themselves to be about as far apart as any group of people can possibly be, yet Rubashov expresses Koestler that there is really no difference between the two. Even the tools of their dictatorships are the same - both have a kind of secret police that make people "disappear" from their homes, both carry out mass executions of anyone they consider oppositional to their ideologies, and both become so wrapped up in the pursuit of their ideology that day to day life for the people is actually forgotten. Koestler often compares the Communists and the Nazis in the narrative of the novel, who are more similar than different despite the fact they are on different sides in the war.