Voyager responds to a distress call, beaming all the people off a Nygean ship that's about to explode. Most are sent to Voyager's cargo bay, but two of them are sent to sickbay, where one takes Seven of Nine hostage. He is forced away from Seven and attempts to take the Doctor hostage. This fails as the Doctor is invulnerable to a common knife.
It turns out that the ship Voyager rescued was carrying prisoners to a facility where they are scheduled to be executed. Since there is no capital punishment in the Federation, the crew are uncomfortable with the situation, but the Prime Directive forbids them from interfering. They provide cages for the prisoners, who are treated brutally by the Nygean guards. Neelix insists that the prisoners must be fed and the Doctor insists they must receive proper medical care. Seven considers this a waste of resources, since the prisoners are going to be killed anyway, but the guards agree to allow the prisoners to have meals.
After a particularly brutal beating by a guard, one of the prisoners, Iko, is seriously wounded. The Voyager guards are forced to rescue Iko by drawing weapons on the Nygean guards.
Due to this brutallity, Captain Janeway orders that Voyager's security personnel take over guarding the prisoners. The Nygeans protest but Janeway gives them no choice.
Iko undergoes a medical procedure in which Borg nanoprobes are injected into his system; not only do the probes repair his injuries, they also seem to have restored the parts of his brain responsible for empathy, and he begins to feel remorse for his crime. At first, Iko wants to be executed for all he has done, but he becomes close to Seven, who sees in him a reflection of her own struggles for atonement for all she did as a Borg. Since under Nygean law, the victim's family decides the punishment for all crimes, Iko eventually appeals to his own victim's family for leniency. He tells them that he is cured, is sorry for what he has done, and that he is hoping to start a new life on Voyager. The family denies his request.
Meanwhile, Neelix becomes friendly with a prisoner named Joleg, who explains that his people are subjected to racial profiling. Joleg persuades Neelix to get a letter through to his brother, but this turns out to be a ruse - Joleg has hidden Voyager's coordinates inside the letter, and the ship is attacked by others of Joleg's race. Joleg has organized a prison break so that his co-conspirators can free him, but the plot is foiled by the Voyager crew. Neelix, who understands that he was being manipulated, turns his back on Joleg.