Responding to a distress call, the U.S.S. Voyager approaches a damaged alien vessel and transports two injured passengers to Sickbay and nine others to a Cargo Bay. In the Cargo Bay, three of the rescued aliens are Nygean guards holding the others prisoner, and they are concerned that their weapons didn't beam over because the other men are dangerous criminals. In Sickbay, another prisoner named Iko takes Seven of Nine hostage and demands a ship and some food. Tuvok arrives with the Nygean warden, Yediq, who says he won't negotiate with criminals. Iko is distracted and Seven breaks free from his grasp. He then grabs the Doctor, but Tuvok fires his phaser through the holographic Doctor and strikes Iko to the floor.
Later, Yediq thanks Captain Janeway for saving them, and he tells her, Chakotay and Tuvok that the prisoners are being transported back to the Nygean homeworld for execution, because they have all been convicted of murder. The officers are uncomfortable that their ship will help deliver eight men to their deaths, but they are bound by the Prime Directive, so Janeway agrees to keep the prisoners detained for several days until a Nygean ship can make a rendezvous. Tuvok outfits the Cargo Bay with prison cells secured by forcefields and tritanium bulkheads, and the prisoners are held there, including Iko, who is beamed over from Sickbay after threatening to kill the entire crew unless he is released.
While Tuvok lays down the ground rules to Yediq, Neelix arrives with a dinner cart. Yediq tells him to take it back because the prisoners don't deserve such an elaborate meal, but Neelix and Tuvok cite Federation protocols regarding the treatment of prisoners, and Yediq relents. Meanwhile, the Doctor expresses to Seven how troubled he is by the captain's arrangements with the Nygeans, because he believes their death penalty is barbaric.
In the Cargo Bay, a prisoner named Joleg provokes Iko into causing a disturbance, and when Yediq checks on him, Iko threatens the warden's children. The Nygean guards enter Iko's cell and beat him severely, but then Voyager security officers jump in and stop the violence. Afterwards Janeway is infuriated with Yediq and bans him and his men from the Cargo Bay, putting Tuvok in charge of the prisoners. The Doctor treats Iko in Sickbay, and asks Seven to provide nanoprobes so he can program them to repair the neurological damage done to the prisoner's brain.
Meanwhile Neelix delivers food again to the prisoners, and Joleg tells him that he ended up among the condemned because he was found in the vicinity of a murder, and was arrested and convicted simply because he is Benkaran — a species "known" by the Nygeans to always be criminal. Later, Neelix contacts the Nygean government under the pretense of a "cultural exchange" and acquires data on their criminal justice system. He tells Tom Paris and B'Elanna Torres that Benkarans occupy a disproportionate amount of space in Nygean prisons, and are ten times more likely to be executed for their crimes than Nygeans. In particular, Joleg was convicted on circumstantial evidence. Paris tells Neelix from personal experience that in prison, "everyone has a story," and to not put too much stock into what Joleg says. But Neelix reminds him that Joleg is sentenced to die.
In Sickbay the Doctor has applied the nanoprobes to Iko, who has woken up in pain, but much calmer than before. The Doctor observes that Iko is now acting grateful and considerate, a stark reversal of his earlier behavior. Iko complains to the Doctor that he is suffering nausea and that he can't stop thinking about the man he killed. Seven believes his discomfort is a manifestation of guilt. Iko's never felt guilt before, and blames the Doctor for making him feel so horrible. Looking at scans of Iko's brain, the Doctor finds that the nanoprobes have established new neural pathways in his brain. While the Doctor gathers more information about Nygean physiology, Iko tries to make conversation with Seven. She is intrigued when he regains his childhood fascination with stars and constellations.
Meanwhile in the Cargo Bay Neelix teaches Joleg how to play Kadis-Kot. In their conversation Neelix learns that the Nygean legal system is based on a principle called "Vekto Valek K'Vadim" — ancient Nygean for "Favor the Victims" — by which the victim's family dictates the convict's sentence. He also learns that if a defendant is wealthy enough, he can negotiate a monetary settlement with the family rather than serve a sentence. Neelix is appalled and wants to help Joleg, but the prisoner doesn't want to do anything that would imply he's guilty. Instead he asks Neelix simply to transmit a letter to his brother.
The Doctor determines that Iko was born with a congenital brain defect that made him prone to violence and sociopathic behavior, and the nanoprobes have inadvertently repaired it. He informs Janeway of this, and she realizes that Iko's "conscience" has been activated. The Doctor believes Iko is no longer a threat, and Seven notes that by some definitions he is not the same man who committed the murder. They tell a skeptical Yediq that Iko has undergone a fundamental change, and killing him won't accomplish anything. They persuade him to work with Tuvok to draft an appeal and submit it to the authorities on behalf of Iko. Iko doesn't want the appeal though, and tells Seven that he deserves to die. He demands to be returned to his cell, where he asks Neelix to give his meal to another prisoner, Egrid, whom he used to always steal food from.
Later, Janeway and Yediq inform Seven that Iko's appeal was rejected. Seven passionately insists on doing more to help him. Janeway realizes that Seven has an issue with atonement, that perhaps if Iko is found not guilty that she herself will somehow be not guilty for the violent acts she committed as a Borg. Just then the ship is jolted by alien fire. The attack causes a power loss in the Cargo Bay holding the prisoners. Joleg and the other inmates, except for Iko, overpower the guards and escape with weapons. The alien vessel tries to beam over the five Benkaran prisoners, but Voyager fires upon the vessel's transporter array and it retreats.
Meanwhile Tuvok tries to neutralize the prisoners in the ship's corridors, but Joleg takes Yediq hostage and demands a shuttle. Joleg backs into the Cargo Bay and has another prisoner seal the door with a phaser rifle. Joleg pushes Yediq to the floor and prepares to kill him, but Iko stops him, saying, "He's mine." Iko takes the phaser and points it at Yediq while Joleg laughs. But then he hands the phaser to Yediq, who immediately shoots down Joleg and the other prisoner. Yediq realizes that Iko really has changed.
Yediq subsequently uses his influence to convince the family of Iko's victim to hear his appeal. Iko speaks to them on Voyager's viewscreen, saying that he will accept death if it helps them find peace but if they let him live, he'll never hurt anyone again. Meanwhile Neelix tells the re-incarcerated Joleg that he found out the "note" sent to his brother was really meant to help him track down Voyager and attack. Joleg tries again to manipulate Neelix, and the Talaxian leaves disgusted. While Iko and Seven look at constellations in Astrometrics, Janeway arrives and announces that Iko's appeal has been denied. Iko must now be detained again and taken home for execution. Seven is devastated, and for at least a day cannot regenerate. Janeway learns that Seven feels remorseful for having murdered thousands without punishment, but Janeway reminds her that she lost 20 years of her life to the Borg, and that's punishment enough.