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At the end of the previous part, Mal had just opened up Simon's cargo crate and found a young woman in cryogenic sleep. The woman wakes up within moments, and we find out that she's Simon's sister. Simon tells the crew about how his sister, River, is a genius. When she was 14, she choose to go to some kind of special government school that would "challenge" her. However, she soon told Simon in code that the school was hurting the students and she needed help. After two years, Simon managed to bribe enough people in the right places to get her smuggled out of the school in cryosleep. From what he learned, the doctors at the school were doing some kind of experiments on the brains of their super-intelligent students. Apparently they aren't willing to let her go, hence the Alliance agent on Serenity.
Simon's talky explanation is nicely cut with scenes of him settling her down after waking up and giving her a sedative to sleep. It underlines the fact that whatever has been done to her has completely destroyed her everyday abilities to interact and take care of herself. Mal declares that if Kaylee survives, he'll leave Simon and River at their next stop; if Kaylee does not survive, then they'll be leaving the ship sooner than that. It's hard to believe even Mal could space Simon and especially River in cold blood - fortunately it never comes to that.
Mal orders Jayne to interrogate Dobson to see how much information Dobson got out in his signal to the Alliance before it was stopped. To Jayne's disappointment, Dobson gives away that no significant information got out before Jayne has the opportunity to use his big knife on him. However, Dobson makes Jayne an offer: go against Mal, help him take River, and Jayne will get lots of money. It's not clear whether Jayne takes him up on the offer or not.
Wash detects a ship approaching, and Mal puts together the clues to realize it's a reaver ship. Reavers are apparently crazy men who are extremely violent, sadistic, and cannibalistic. Mal decides the best course of action is to continue on their passing course, as turning and running could provoke the reavers to come after them. He tells the crew, and we see how deeply frightened they are. Zoe tells Simon that if the reavers catch them, they will rape them to death, eat their flesh, and sew their skin into their clothes. We see Inara and Jayne separately preparing suicide methods for if they are boarded. Fortunately, the reavers pass by. In other good news, Kaylee is awake and appears to be on the way to a full recovery.
They reach their destination world, and Mal makes plans for how they will convey the goods to their buyer, Patience, since Mal expects a double-cross. We get a good look at how Mal has retained his soldier training, as he picks out the exact locations on the surrounding hills where snipers will be placed and reads the terrain to tell where Patience and her men will come from. We also see just exactly what Jayne was hired for: Mal tells him to neutralize the snipers without giving himself away, and he does it with no problem.
When Patience and her minions arrive, Mal gives her a sample of the goods. This was an interesting surprise: we find out that the stolen items are some kind of concentrated food bars that could feed many people for quite some time. Patience gives Mal the money, and Mal tells Patience where the rest of the food bars are. But Mal was right about the double-cross: Patience demands her money back. Mal actually does give her the money back and Jayne demonstrates that he controls the sniper rifles, but even so, Patience and her men start a fight. Zoe is shot, but we learn she has a bulletproof vest. Between her, Mal, and Jayne, Patience's men are all shot. Mal shoots Patience's horse so it pins her, and then he takes the money and leaves her.
Meanwhile, on Serenity Dobson has managed to untie himself. He knocks Book unconscious, and then snatches River and holds her hostage with a gun. Simon manages to get one of his two guns and they are in a stand-off. On the bridge, Wash detects the reaver ship bearing down on them. He contacts Mal; fortunately, Mal and the others are already on their way back. He notifies the crew that they will be fleeing momentarily.
When Mal returns through the ramp up into the cargo bay, Simon and Dobson are still in a stand-off. Mal puts an end to this by shooting Dobson in the head, just over River's shoulder. Since earlier Mal had agreed that it would be stupid to shoot an Alliance agent, we see just how desperate their need to flee the reavers is. Dobson's body is unceremoniously dumped off the ship, and they take off. Mal orders the "civilians" into Inara's shuttle so they might be able to escape if the reavers seem to be about to catch them; Simon and River go with her, but Book decides to help Kaylee. Kaylee is carried to the engine room by Jayne so she can do whatever is necessary to facilitate their escape. With Wash's piloting talents and a dangerous maneuver, they manage to evade the reaver ship and leave the vicinity of the world.
Now everyone has to recover from the narrow escape. Zoe and Wash head to their cabin so Wash can tear off Zoe's clothes. We see Inara and Book in Inara's shuttle. Inara is fixing Book's injury from Dobson's escape. Book says he's not sure he's on the right ship because of all that's happened to him and around him already - he's most disturbed by the fact that he doesn't necessarily think Mal was wrong for killing Dobson. Interestingly, Inara gives Book encouragement and direction: the scene is even set up as if Inara was giving Book a blessing.
Mal tells Simon that the ship could use a doctor, so if Simon and River want to stay, they are welcome to. Simon is surprised, to say the least, but despite the life on the run that Serenity offers, it's clear that it could also keep them ahead of the Alliance. Simon agrees.
This episode really shows the danger and capriciousness of life on the frontier in this planetary system. We see Patience, the "mayor" of her world, acting no better than a mafia boss. We see the reavers, which clearly inspire terror, doing whatever they wish without being stopped by the Alliance. We see that the high-value stolen goods Mal sells are foodstuffs. There's obviously a certain excitement to living a life on this frontier, but it also seems like that life could be very short.
One of the most pivotal events in the episode is Mal's decision to harbor Simon and River. Why does he do it? His statement that they need a doctor is a flimsy excuse, when they have managed to survive so far without one. I suspect that since the Alliance wants River, Mal naturally wants to keep her from the Alliance. Does he have any idea what he's getting into? Just what has been done to River, and what is she capable of?
The relationship between Mal and Jayne is an interesting one. Jayne clearly did not accept Dobson's offer to turn on Mal; we were kept in suspence about it for awhile as Jayne eyed Mal through the sniper rifle during the deal with Patience. Later, Mal asked Jayne why he didn't accept Dobson's offer. Jayne is obviously taken aback by this a bit, since Mal was not listening to that conversation. This was a clever (and probably obvious) deduction on Mal's part, but by asking Jayne about it, he lets Jayne know that he's smarter than Jayne, and he's always got his eye on Jayne. As Jayne says, if he ever gets an offer that is good enough, things will get very interesting.