Crime and Punishment primarily delves into the theme of a guilty conscience. For Dostoyevsky, punishment transcends physical actions or conditions. Much like Milton's epic poem Paradise Lost, punishment is a natural outcome of being aware of one's guilt. Guilt involves recognizing wrongdoing and feeling estranged from both society and God. From the beginning of the novel, Raskolnikov (whose name originates from the Russian word for "schism") experiences this estrangement. By killing the pawnbroker, he attempts to demonstrate superiority over the law, but the murder only intensifies his sense of alienation from society.

Sonya, despite being a prostitute, represents innocence. Her choice to engage in prostitution is not motivated by lust. In fact, throughout the novel, there is no suggestion that Sonya harbors any lustful or sexual desires. Instead, she feels embarrassed and ashamed of her profession. In Dostoyevsky's perspective, she is not guilty of any sin. Her actions are driven by necessity, not by base instincts or selfish motives.

In contrast to Sonya's shame, Pyotr Luzhin is unashamed in his manipulation of Raskolnikov's sister and mother (Dunya and Pulkheria Aleksandrovna). He is guilty of emotional manipulation and deceit. Arkady Svidrigailov is even more culpable. While Luzhin's offenses are calculated, Svidrigailov's arise from his complete surrender to his evil inclinations. Unlike Raskolnikov, who ultimately confronts his guilt and its repercussions, Svidrigailov only partially acknowledges his wrongdoing and evades consequences by taking his own life. Although Raskolnikov is the main character in Crime and Punishment, Dostoyevsky implies that he might not be the novel's most guilty character. Svidrigailov and Luzhin also commit criminal acts and are less open to redemption than Raskolnikov.