Shon, a young alien boy, has developed a "congested blockage in his upper air passages." When Dr. Franklin explains to Shon's parents that Shon's condition can be cured by a fairly routine surgical procedure, the parents seem bewildered. "You will cut him open?" they ask, and explain that the "Chosen of God" cannot be "punctured" - for their souls will escape.
B5 has received a distress signal from the starliner Asimov, which has been immobilized because of a fire in its command and control center - unfortunately, the ship is now adrift in Raider territory. Ivanova (who pleas with Sinclair to send her instead of Garibaldi) is sent to lead a fighter wing to rescue the Asimov.
Dr. Maya Hernandez, one of the B5 doctors, tries to convince Shon's parents to allow the procedure, but they are quite determined not to allow it. Just as it becomes evident that the parents will not change their mind, Franklin suggests an alternate procedure. He admits that this procedure won't work as well, but it's better than nothing. After the parents leave to consider this new method, Dr. Franklin explains to Hernandez that, though this procedure will obviously not save Shon, it will at least give Franklin time to try to convince the parents to change their mind. Both doctors realize that there are only two options - surgery or death - but Franklin explains that it is sometimes necessary to "heal the family before you can heal the patient." Shon's parents return and say that they are willing to try Franklin's new procedure.
Franklin, who is speaking with Sinclair, explains his dilemma. Franklin requests that Sinclair order him to perform the surgery, but Sinclair declines, commenting that it's a dangerous precedent to set. Franklin explains that that precedent has already been set - by Sinclair's ordering Dr. Kyle to save Ambassador Kosh (cf. "The Gathering") - and when Franklin brings up the idea of making this issue official by petitioning Sinclair with a formal request to operate, Sinclair asks him to try to find another solution.
Meanwhile, Franklin's "procedure" is obviously not working. When the parents become angered, Franklin pleads with them again, but they still refuse to allow surgery. Finally, Franklin threatens to suspend their parental authority if they will not allow him to operate - and he makes a formal request for Commander Sinclair to decide this issue.
Shon's parents go to Sinclair and request that he decide in their favor. Sinclair explains his dilemma - he must consider Franklin's request, but he must also act as the parents' advocate because the parents' race has no ambassador on the station. The parents express their objection - they don't like the situation and believe that Sinclair will rule against them because "Earth people always stick together."
The parents visit Ambassador G'Kar and ask for the Narn to intervene on their behalf, but G'Kar claims that the parents' world doesn't have much to offer to Narn - and claims the Narns don't casually enter into other people's affairs. The parents then visit Ambassador Mollari, who says that he sympathizes with them but explains that it would be too expensive to intervene - if the Council was called on this matter, there would be a whole array of costs that would have to be justified. Ambassador Kosh proves just as unhelpful to the parents: concerning the issue of a patient's safety versus the concerns of the patient's world, he simply says, "The avalanche has already started. It is too late for the pebbles to vote."
When the parents plea with Delenn, she says that she sympathizes entirely, but she also says that the Minbari are reluctant to get involved with the religious affairs of other people - especially because they've seen what happens when other races interfere with Minbari religious affairs. Delenn explains that both Dr. Franklin and the parents believe they are doing what's "right" - yet how can either of them prove it?
Meanwhile, Ivanova's team has found the Asimov - but they have also picked up the signal of an approaching Raider vessel.
Sinclair explains to Garibaldi how distraught he is - the buck keeps being passed back to him. Earth Central refuses to advise, and the other ambassadors refuse to take action. Later, when Sinclair visits Shon, Shon explains that, though he doesn't want to die, he doesn't want the surgery either.
When Sinclair finishes speaking with Shon, Dr. Franklin asks him what his decision on the request will be. Sinclair explains that it's a difficult decisions: both sides, according to their own beliefs, are morally "right." "Who should I believe?" asks Sinclair. "You [Dr. Franklin], because we share the same beliefs? Or do we? ... What makes a religion false? If any religion is right, then maybe they all have to be right. Maybe God doesn't care how you say your prayers, just as long as you say them ... What we hold sacred gives our lives meaning. What are we taking away from this child? ... I have to refuse to sign the order. I can't allow you to perform the operation."
When Franklin angrily confronts Sinclair, Sinclair explains that he really had no choice in the matter. According to his personal beliefs, he would sign the order right away - but as commander of B5, he wants to ensure the neutrality of the station. He explains that he can't just set other races' beliefs aside whenever it's convenient or whenever they violate human beliefs. He also says that, though he is violating the precedent set when he ordered Dr. Kyle to operate on Kosh, that particular precedent must be stopped somewhere.
Meanwhile, Shon's condition is worsening. Franklin calls Shon's parents, who say how grateful they are for Sinclair's wisdom, and who tell Shon how proud they are of him that he is dying honorably. When Shon's parents leave, however, Franklin decides to operate on Shon anyway - he can't allow a simple legal order to get in the way of what's "right," according to him. Dr. Hernandez decides to help him.
The Raider ship that is approaching Ivanova is meanwhile getting closer. Ivanova, in defiance of general orders to the contrary, breaks formation and pursues this Raider ship - as the rest of the squadron escorts the Asimov back to B5. Ivanova successfully destroys this ship, but notes a large squadron of Raider ships approaching after her. She reverses her thrusters, trying to escape.
Franklin's operation was successful, and Shon - who is now physically fine - comments that he doesn't feel spiritually any different than he did before. When his parents arrive, however, they angrily shun Shon - they treat him as if he were some sort of evil demon and try to exorcise him.
Sinclair, when he hears, angrily confronts Franklin. However, they are both interrupted by Hernandez, who summons them to the Med Lab. At Med Lab, the parents have again arrived - and this time they appear a little more complacent. They say that if it were in their power to forgive Franklin, they would - because he meant no harm, and because he did what he did out of compassion. They leave, after wrapping Shon in a "travelling robe."
A little later, when Franklin and Hernandez are researching the customs of Shon's race, Franklin comes across a description of a "travelling robe." Suddenly, he rushes out of the Med Lab, runs through the corridors, and arrives at Shon's room - only to realize that he is too late, that the parents have already killed Shon. The parents, however, don't see why Franklin is so upset - they comment, "This was not our son. This was only a shell. There was nothing to do but end the pain of the shell."
Later, Sinclair tells Franklin that he won't ask for his resignation - this time. However, he comments that Franklin shouldn't have made the request - then, he wouldn't have had to violate it. Franklin is quite upset with himself, however, for not knowing that the parents would kill Shon. Franklin wonders if things might not be better or easier if nobody cared about life or religion.
"What makes us human is that we care - and because we care, we never stop trying," replies Sinclair.
Meanwhile, Ivanova and her squadron have returned safely. When Garibaldi asks her about the orders she violated, Ivanova explains that sometimes things work out when one takes an educated risk. Garibaldi replies that at other times, they don't - and he explains the events of the preceding days to Ivanova.