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Dr. Franklin and another doctor, Dr. Hernandez, are examining a young boy, Shon. Shon and his parents are of a species we have not encountered yet, and we get the impression that their people do not travel off-world much, since they do not even have an ambassador on the station. Shon has a lung problem that will kill him within a few days, but that is easily correctable through a simple surgical procedure. However, the religious beliefs of Shon and his parents prohibit the body from being punctured, lest the spirit escape from the body.
Franklin can hardly believe his ears when the parents forbid surgery, but convinces the parents that there might be a slower, non-surgical method to heal Shon. Hernandez calls him on this - in reality, he's just trying to keep the parents around in the hope that they will get desperate and reconsider the surgery. And in reality, the boy is not likely to survive a journey to find another doctor.
Franklin confers with Sinclair and Garibaldi, explaining the situation. He asks Sinclair to order him to disregard the parents' wishes and conduct the surgery, pointing out that Sinclair has already set the precedent of personal survival being paramount when he ordered Dr. Kyle to examine Kosh in "The Gathering". Sinclair refuses. He could've pointed out that their were larger issues at stake in Kosh's case, such as possible galactic war if Kosh died, but I think he realized that kind of reasoning would be wasted on Franklin.
Shon's condition worsens, and his parents realize that Franklin's alternative method isn't working, but they still refuse the surgery. Franklin is desperate himself, and tells them that he is going to request that Sinclair override their decision. The parents panic, even though Sinclair tries to convince them that he's going to weigh both sides and do his best to make a fair decision.
Since the parents do not have an official ambassador, they begin visiting the ambassadors of the major races seeking intervention. G'Kar tells them that if they don't have anything to offer the Narn, then the Narn will not get involved. Londo smoothly sympathizes with them, but says that the cost of the research and paperwork needed to intervene would be too much. Surprisingly, Kosh listens to the parents, but gives one of his enigmatic statements, which doesn't help them. (It's a bit obvious, but still amusing when the parents ask Kosh to imagine that he himself were in their situation, because of course he was. We never really heard how he feels about Sinclair's actions.) Delenn sympathizes with them, but she's the only one that sees to the heart of the matter: how can an outsider say which belief system (human or alien) is correct? In the end, she says she cannot judge.
Sinclair visits Shon in medlab. Shon says that no, he doesn't want to die, but he also doesn't want to go against his beliefs. Sinclair spends some time as Shon tells him about his religion. In the end, Sinclair rules that the parents should decide about the care of their son, so if they forbid surgery, Franklin can't do it. Franklin is shocked, to say the least, but Sinclair realizes there's a bigger issue involved than the life of one child. Sinclair can't go around the station pushing human religious beliefs on the alien races, or he'll compromise the station's mission.
Shon's parents pay him what may be their last visit, since his condition is getting worse rapidly. As soon as they leave, Franklin preforms the surgery anyway. It's spectacularly successful. When Shon wakes up, he realizes what's been done, but says he doesn't feel any different.
When Shon's parents arrive and see him feeling much better, they immediately begin warding off evil spirits and feel from medlab, leaving Shon in tears. Sinclair is notified and calls Franklin in for a serious and angry lecture. They are interrupted by a call from medlab.
When they return there, Shon's parents have arrived, and they are much calmer. They say they are ready to take Shon with them, and have even brought a ceremonial robe for him. When they leave, Franklin is hugely self-satisfied, although Sinclair is still simmering. Franklin's satisfaction is short-lived, however, since he happens to read some information on exactly what the ceremonial robe is for. When I first saw this episode, I didn't realize until Franklin did what was going to happen. His desperate run through the corridors to stop the inevitable gives us a moment to digest the impact of what he knows is happening - and then we arrive at Shon's quarters to find him already dead on the bed, very peacefully composed. The parents are surprised at Franklin's dismay, since Shon's body was only a "shell" that they were putting out of its misery. Shon's spirit had already left, during the surgery.
Later, Franklin and Sinclair commiserate together. Sinclair has decided not to demand Franklin's resignation - I think he realized that Franklin is punishing himself enough. Franklin is seriously depressed, as he should be.
A subplot throughout the episode involved rescuing a damaged passenger liner before raiders can attack it. Ivanova leads a squadron of starfuries. They encounter a number of raiders, but manage to get the passenger liner safely back to the station.
This episode was horribly tragic, since the poor Shon was doomed to death no matter what happened. The situation really came down to the question Sinclair and Delenn enunciated: how do you know whose belief system is correct? From the point of view of most people watching this show, the idea of withholding medical care from a child is horrifying. However, that's because the majority of mainstream beliefs on Earth say that using medical care is OK. There are a few religious groups that are classified as "fringe" or "cult" that do not allow medical treatment, and most people consider them to be at least a little crazy. In fact, because of most humans' beliefs, it's illegal in the United States to withhold medical care from a child. (I think, but I do not know for a fact, that it's legal to refuse medical care for yourself if you are an adult.)
But who's to say that the mainstream religious beliefs that allow medical care are correct? What if the "fringe" groups that forbid it are really doing what God wants? The entire basis of religion is that it must be taken on faith: there is no proof of the basic tenets of the religion. So if a religion forbids medical care and relies solely on prayer, how do we know it's wrong? No one can prove any religion is correct.
I would contend that if God could be scientifically proven to exist, then a belief system based on him would no longer be a religion. Instead, experiments could be done and measurements made to determine the properties of "God", and we would build up a body of facts about him. That would remove the requirement of faith from the equation, since we would have scientific means of predicting and explaining what God does, and the knowledge would be like knowing the Sun was going to rise in the morning - something we take for granted. There would be nothing to doubt, and so no faith would be required. That's not much of a religion.
Incidentally, we have no indication that Shon's parents are considered "fringe" or "fundamentalist" within their own culture. They claim that if they had an ambassador, she would completely support them. In fact, they may be somewhat liberal since they have traveled off-world to look for help instead of accepting their own doctor's prognosis.
One of the more interesting scenes is when Franklin is defending his defiance of Sinclair's orders. Sinclair asked him, "Who asked you to play god?" And Franklin replies that every single one of his patients do, when they desperately want to be healed. That comment really strikes home. Hernandez had earlier commented that Franklin's "religion" was medicine, which Franklin scoffed off a bit, saying that medicine has testable, reproducible results (and hence is a science). But for the majority of us that do not understand the details of medical treatments, medicine can sure look like magic or a miracle. Franklin's defense to Sinclair is that if his patients are going to ask him to ask like God, then he's going to claim God's authority, too - and so he performed the surgery. This is such a wonderful, raw scene.
These issues make for a very compelling and heart-wrenching story. Even if you believe as the parents do, they are still watching their child die, and they are torn apart by it. There's no doubt in the episode that the parents love Shon; but they aren't willing to risk his spirit when the life after death they believe in depends on his spirit.
Sinclair makes the only decision possible, although I don't envy him having to make it. If the episode had stopped there and Shon had died, it would have been tragic enough. But having Franklin "save" Shon only to have him killed by his own parents just twists the knife for the viewers. Naturally, we can't help but believe Shon was perfectly fine after the surgery, and how could the parents not see that?
This is one of the best moral and philosophical episodes of the series, and it's a tear-jerker for me every time. It makes me thankful that I am not a doctor, and so I don't have to worry about these issues.