The themes of atonement and forgiveness are closely connected to notions of guilt and innocence. Dostoyevsky's title suggests that punishment is the inevitable outcome of crime. However, punishment transcends legal judgments and prison sentences. In Dostoyevsky's view, the real punishment for a criminal is not just incarceration. Legal repercussions alone cannot fully address crime. The true punishment arises from the criminal's conscience and their awareness of guilt. To genuinely confront this guilt, the criminal must acknowledge it, atone for it, and seek forgiveness.

At first, Raskolnikov tries to justify his crime with various reasons. The most significant is his "superman" theory. By its nature, this theory dismisses the need for atonement. According to the superman theory, a superman can commit any crime to achieve his objectives without needing to atone. Raskolnikov also rationalizes his crime by claiming the old pawnbroker is worthless to anyone, and by killing her, he is removing an undesirable person from the world. Additionally, driven by poverty, he argues that he plans to use her money to improve his life. As the story progresses, he comes to realize that none of these justifications can excuse his actions.

Raskolnikov's fear of arrest is multifaceted. It becomes clear that without Sonya's guidance and support, he would be unable to seek forgiveness. Remarkably, when he confesses his crime to Sonya, she forgives him immediately. She encourages him to bow before God and make a public confession, believing this act of repentance will help him start to purify his soul.

Svidrigailov, in contrast, recognizes his guilt but does not seek forgiveness. Unlike Raskolnikov, he does not believe in the possibility of redemption. He attempts a form of atonement by giving money to Sonya and others, but even these gestures are partly motivated by self-interest. Feeling spiritually dead, he concludes that the only way to atone for his sins is through suicide.