"In the Penal Colony" revolves around the rather, um, unique system of justice and punishment used in the place where it is set. The judicial system of this penal colony is based on the idea that, as one character says, "Guilt is never to be doubted." The accused are never tried nor given an opportunity to defend themselves. Instead, they are simply put to death at the order of the judge in an elaborate and apparently brutal fashion. The explorer visiting the colony finds the execution procedure unjust and inhumane to the extreme, but the officer who defends it reveres it as the highest kind of justice. How could it be seen as just?
The officer believes "guilt is never to be doubted" because he believes all human beings are guilty.
The officer regards the colony's justice system as perfect because it allows no disagreement among people about what is just and unjust.