Frustration and Meaning
As each character's desires emerge, it becomes clear that each person's desire is frustrated by the others. This prevents them from finding meaning. The Condemned Man wishes for freedom, but the Soldier and Officer need for him to die and have a religious experience. The Traveller is confounded by the Officer's sincere defense of the apparatus and knows he must report to the Commandment in a way that upholds his integrity. The Officer wants both favor from the Traveller and to continue torturing the condemned prisoners, but upon realizing the hopelessness of his operation, he turns the machine against himself. It malfunctions and kills him without allowing him the religious experience of death.
This theme is poignantly resonant of Kafka's own struggle to find meaning in his life. It's ironically self-defeating and emphasizes his message that meaning in life is often blocked, leading to deep, even fatal frustration. If meaning is attainable, it is only by perverse means, and is usually directly opposed to someone else's joy.
Religion
The Officer's ironic death serves to raise moral questions about religion and the meaning of life. In a sense, the Officer serves as a Christ figure, because his torturous death saves the life of someone who was condemned to die. However, because the Officer chooses torture out of his own desire to affirm the value of the apparatus, which makes him self-serving, rather than selfless like Christ. Thus, he is punished with a quick and brutal death rather than the drawn out and redemptive one that Christ had.
Life as slow torture
The image of a slow, torturous death may seem to be only about the death of the mortal body, but it also brings up questions about psychic pain. Perhaps Kafka intended the apparatus' torture as a symbol for life itself: a slow, drawn-out process ending in death, with much mental as well as physical pain.
Religious Enlightenment in Death
One of the moral arguments the Officer uses to convince the Traveller that the torturous death at the hands of the apparatus is not immoral or excessive is that the slow, torturous death provides the dying man with a religious experience that redeems their sorry fate. His decision to die by the torture machine shows how committed he is to this belief.
The Officer claims that the point of death is that it leads to a transcendent religious experience that validates the pain and frustration of life. The fact that the Officer, who maintained that argument, dies quickly and brutally rather than being shown to have a religious experience while being tortured to death suggests that we ought to take this idea with a healthy dose of skepticism.
Power and Punishment
Kafka probes the nature of punishment in this story, especially as it relates to the power structure of the society it takes place in. His penal colony is a place where those in power maintain that there is perfect order and justice, but in reality it is clear that both are lacking. Discipline in the penal colony is enforced through the spectacle of punishment through the apparatus. Specifically, punishment is levied through the destruction of the body, for the body is ultimately the means by which those in power get to control the hearts and souls of those they rule. Those in power maintain their grip on society by insisting that their method of punishment is good for the people, since it supposedly results in religious transcendence.
The Fallacy of Narrative
"In the Penal Colony" makes us question whether narratives can ever really result in a clear and meaningful conclusion. The Officer spends much of the story building up the power of the apparatus, telling the Traveller about the apparatus' perfect functioning, the Old Commandant's genius, the religious transformation that takes place for those the apparatus is used on, and the popular appeal of watching executions in the old days. However, all of this proves to be nearly completely false. His narrative is ultimately proven wrong when he uses the apparatus on himself and it malfunctions and falls apart. All his talking had no effect on reality, and did nothing to change the Traveller's mind or his own fate.
Justice
A major moral question raised by "In the Penal Colony" is how justice should be carried out in a well-functioning society. The system of justice in the penal colony denies those accused of a crime to the chance to defend themselves, and seems to require the death penalty for even minor infractions. From Kafka's narrative choice to have the Officer brutally killed by his own apparatus, it can be gleaned that he does not believe this is a proper way for justice to be served. The narrator's fixation on the Condemned Man's lack of understanding of his crime and upcoming punishment shows that Kafka favors a system of justice in which someone must understand the law that they have broken to be convicted of a crime, and which allows them the chance to defend themselves. Furthermore, scholars have argued that the way the apparatus is depicted amounts to an argument against the use of capital punishment at all (Dragich).
