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Serenity arrives at a back-water world to deliver the cargo of the previous episode: cattle. Mal still has to conclude the deal with the local buyers and he doesn't want River pulling a crazy fit, so he sends Simon and River into town.
"Town" turns out to be about a dozen buildings on one dirt street - possibly the most primitive frontier town we've seen so far on the series. Kaylee and Inara are browsing in the general store and Simon and River arrive. Simon is frustrated by keeping watch over River (reminds me of supervising my kittens!) and accidentally spouts out his general dislike for being on the run, frontier planets, living on Serenity, and Mal. Kaylee, who has been nursing a crush on Simon, is hurt by his dislike of the life she lives, and she and Inara leave.
Before Simon can try to fix the situation with her, he realizes River has disappears. He tracks her down to an outdoor party - probably some kind of wedding party with lots of dancing. River jumps right into the festivities, and Simon relaxes for a bit as he enjoys River's happiness. When the dancing ends, he is kidnapped by men from a local community of settlers. When River tags along, they take her captive, too. Just as Simon says that the crew from Serenity will rescue them, we see Serenity fly away.
While Simon and River were away, Mal's dealings with the local buyers did not go well. He had just negotiated a deal with them when the local sheriff and his posse show up to arrest the buyers for some local crimes. A firefight ensues between the sheriff's men and the buyers, but eventually the sheriff gets his men. Unfortunately, Book is shot in the chest during the fight. Mal and the rest of the crew load Book onto Serenity and take off immediately to find medical help. Zoe does what she can for Book, but she doesn't have the skills to save him. Many of the crew are upset at abandoning Simon and River, but they've discovered that they aren't in town and were likely abducted by the settlers, who have a reputation for such.
There aren't any worlds close enough with adequate medical facilities, so against his better judgment, Mal is forced to approach the local Alliance cruiser and beg assistance. A squad of Alliance soldiers board Serenity to find out what they want. The officer in charge is about to turn them away when Book asks him to check his identity card. Whatever is on the card must be good, since the officer immediately orders help for Book and allows the rest of the crew to stay while he's being treated. Fortunately, the doctors are able to stitch Book back together. When he returns to Serenity to recover, Mal tries to find out what it is in Book's past that gained him such regard by the Alliance, but Book refuses to tell him.
Back on the planet, Simon discovers that the settlers kidnapped him because they are in desperate need of a doctor. A woman named Doralee has been acting as a nurse, but she doesn't have the knowledge to take care of the settlers' illnesses. We can see Simon's heart soften a bit at the settlers' plight, although he still complains repeated about being abducted. He begins tending the sick with Doralee and River's help.
The situation seems to have settled down somewhat. River even has a relatively lucid period, where she tells Simon she knows how much trouble he's gone through for her, but she's still so mixed up from what the Alliance did to her. It's about time that we saw some progress in River's condition, in order to have hope that she's not going to just be crazy girl all the time. Then River begins revealing information that she apparently got via telepathy. (We'd had some hints at that in "Shindig", but it wasn't certain.) Doralee pronounces River a witch and calls the village leader. River unwisely reveals compromising information about him, and he also declares her a witch and the village prepares to burn her at the stake.
Simon desperately tries to stop them, but his words fall on deaf ears. I don't know why he didn't threaten to withhold medical care from them (like he did with Mal when Kaylee was shot in "Serenity", part 1) - maybe he thought they wouldn't care. In the end, he gives up and joins River on the pyre waiting to be lit. Serenity shows up and Jayne from the ship and Mal and Zoe from the ground storm in and rescue Simon and River. Once back on the ship, Mal tells Simon that he rescued them because they are part of the crew; we can tell that that means everything to Mal.
Throughout the episode, we had flashbacks from Simon to his childhood with River. We get a nice look at River as a precocious, imaginative child and Simon as the perfectly-mannered and dressed older brother; their family appears to be rich, but not overly snobby, and indulgent of the children. We see how that changes when River goes to the "special" school and Simon first gets the signs that something is wrong. His parents think he's being paranoid, and by this point they have become very status-conscious. They are worried about Simon losing his doctor position and about the bad publicity his rash actions might cause for the family's reputation. In the end, we see Simon's father essentially disown him.
The flashbacks really helped flesh out the back story that Simon gave in "Serenity", part 2, as well as making it easier to relate to. I wish we'd had one more scene with River and Simon slightly older than the first when they were children. At any rate, we get a much better feel for the bond between them and the lengths to which Simon had to go to rescue River. His comment to his father that he didn't know their family would be so easy to break apart was particularly painful.
Simon's status as part of Serenity's crew has now been established, but it's not clear when Mal decided this. When Serenity originally fled to find help for Book, Mal seemed ready to wash his hands of River and Simon. We don't know what changed his mind - did Book say something after he came back from the Alliance ship? I also think Mal feels somewhat responsible for the fact that Simon wasn't around to help Book, since Mal did, after all, chase Simon and River away to town.
One can feel for the desperate need of the settlers for a doctor, but with their overly suspicious mentality, I couldn't feel too sorry for them. It's so hard to believe that in a time with spaceflight and colonies on many planets that such superstitions could exist, but many people choose to be ignorant.
The big mystery of the episode is what Book did in the past. We already know that he is more knowledgeable about tactics, hand-to-hand combat, and Alliance ways than one would expect as a simple preacher. I suspect he was previously some type of Alliance operative or soldier - apparently a really good one, or high-ranking - who did something he couldn't live with, which lead him to turn to a life of as pure goodness as possible. Will Book be willing to help Mal out in Alliance matters in the future?
One bit in the episode that I found amusing was Jayne's reaction to Simon and River being left behind. Obviously, he has thought they are trouble, so he was happy. But he immediately begins ransacking their rooms and stealing whatever he wants; his "reading" from Simon's diary was hilarious. When Simon and River return, he quickly dumps their belongings back in their room - does he think they won't notice?