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Serenity arrives on Ariel, a core world deep in Alliance territory. They are there to drop of Inara for her yearly required physical examination as a registered Companion. Book was dropped off en route at an abbey to visit. This episode clearly takes place quite awhile after the previous episode ("Out of Gas"), where they were far out in the system avoiding contact with everyone.
The crew are contemplating what they will do during their time on Ariel. Zoe refuses to step out of the ship, saying that she doesn't want anything to do with such a tightly Alliance-controlled world, despite Wash's urgings to have fun. Mal orders everyone to stay put and out of sight on the ship to avoid trouble. For no reason, River picks up a carving knife and slashes Jayne across the chest. Simon fixes Jayne up, but Jayne is furious and demands that Mal leave Simon and River on Ariel. Mal refuses, saying that they are part of the crew; but once Jayne leaves, he tells Simon that River must stay in her room at all times unless escorted. Simon reluctantly admits that River's state of mind has been deteriorating.
Shortly thereafter, Simon surprises Mal and the others by telling them he has a job for them. He proposes that they go to a major hospital in Ariel City, where he will direct them on what drugs to steal - drugs that are worth a fortune on the frontier worlds Serenity usually frequents. (In a nice bit of continuity, the worry that stealing the drugs could hurt patients is assuaged by noting that on a core world like Ariel, the drugs will be replaced rapidly.) While at the hospital, Simon will secretly scan River with a brain-imager, which he hopes will give him some clues on what was done to her and how he can more effectively treat her. This heist will be no simple job, but Simon has obviously put a lot of thought into how they can do it.
While he details the plan, we see the preparatory parts in action, which is a nice way to keep the exposition moving. Kaylee and Wash procure a discarded ambulance ship, which they fix up; some of the crew will play paramedics, bringing in patients. The appropriate uniforms and IDs are also acquired through shady means. Some humor is provided with Simon training Mal, Zoe, and Jayne on what to say in their role of paramedics bringing in dead-on-arrival patients - apparently there is no equivalent of ER in the Firefly universe for them to have gotten familiar with all the medical terms, because they all have a horrible time memorizing their parts. Simon and River will be given certain drugs so that they appear to be dead, but they will be revived once everyone is in the hospital.
The plan starts out well, as Mal, Zoe, and Jayne don't even have to use their lines, although Jayne insists on spouting his off anyway. Once everyone is in the morgue, they split up. Mal and Zoe follow Simon's instructions on where to go to steal the drugs, which they put in a hard-shell body bag. Jayne is left to revive Simon and River and escort them to the brain imager. This is the the only bit of the plot that I have a problem with - why does Mal trust Jayne out of his sight. I would have thought Mal and Jayne might get the drugs, and Zoe go with Simon and River. There's no obvious reason that Jayne couldn't go with Mal, beyond the fact that Mal is comfortable working with Zoe.
Before Jayne revives the "corpses", he contacts an Alliance agent to confirm his deal of turning Simon and River in for the reward. Once Simon and River wake up, they pose as a doctor and paramedic escorting a patient in a wheelchair. Simon pauses to save the life of a patient from the ministrations of an incompetent doctor - just a taste of what Simon's life might have been like if he hadn't given it up to save River.
Simon successfully scans River with the brain-imager. I have to say that the imager as depicted was very cool: it gave Simon a 3-D image of River's brain that he could "grab" and rotate. Just his cursory examination gives him vital information on what was done to River. The doctors at the "school" operated on her brain several times, removing a crucial part of her brain that buffers emotions. Instead of being able to mute and control her emotions, she is forced to act on them constantly. No wonder she appears so capricious and crazy.
After the scan, Jayne leads Simon and River into the trap with the Alliance agents. Simon and River are handcuffed and led off; the head agent also arrests Jayne - when Jayne demands his reward, the agent says that he'll be taking it himself. When Jayne is put into holding along with Simon and River, Simon thanks Jayne for not trying to escape without them and leave them behind. When two guards escort the prisoners to a cell, Jayne and Simon manage to attack them and escape.
Meanwhile, Mal and Zoe have returned to the ambulance ship with the loot, but realize something is wrong when the other team does not return. Wash (in the ambulance ship) and Kaylee (on Serenity) monitor local communications, which clues them into the fact that Simon and River have been captured. They also access hospital plans in order to direct Mal and Zoe to where the others are likely being held.
The situation becomes more urgent when special Alliance agents arrive to take Simon and River. River somehow senses them and begins to panic, leading the others away from the special agents. She repeats her "two by two, hands of blue" rhyme from "The Train Job".
We see that there are in fact two special agents, and their hands are blue. They proceed to kill the Alliance agents involved with the capture of Simon and River, simply for talking to them. The weapon they use appears to be some kind of ultrasonic device; my conjecture is that somehow the vibrations liquefy soft tissues in the body, as we see the victims bleeding from the eyes and nose. Why aren't the agents themselves affected, despite being in the same close proximity?
Jayne, Simon, and River run into Mal and Zoe, and they all successfully return to the ambulance ship and then to Serenity. Inara has also just returned, and they leave Ariel immediately. Simon praises Jayne highly for saving them from the Alliance agents and not just saving themselves.
Mal knows Jayne better, though, and once the rest of the crew leaves, Mal knocks Jayne out and them traps him in the outer part of the cargo hold. Jayne comes to, and Mal opens the cargo hold door while Serenity is still ascending through the atmosphere. Via intercom, Mal demands that Jayne tell him the truth about how the Alliance agents caught them. Initially Jayne denies snitching, but he breaks down pretty quickly with the imminent departure of Serenity from the atmosphere. He admits arranging the deal with the Alliance, but then says he got stiffed. Mal is furious, telling Jayne that betraying a member of his crew is like betraying Mal himself. Mal walks off, leaving Jayne to his fate. In the end, Jayne begs Mal not to tell the others that he betrayed them; I think this makes Mal change his mind, as it's at this point Mal closes the cargo door, sparing Jayne's life.
So much happens in this episode with both recurring plots and the characters. First, it's satisfying to finally get some explanation of what the Alliance did to River to cause her current condition. It also provides a plausible basis for Simon to begin treating her. However, removing part of River's brain does not explain some of her unusual abilities. As we saw in "Safe" and possibly also "Shindig", River seems to be able to read minds. Recently, we have also seen some evidence for precognition: in this episode, she knew the doctor Simon ended up helping was going to accidentally mistreat his patient; in "Out of Gas", she said "fire" just moments before the explosion that crippled the ship. What else did the Alliance do to her?
Way back in "Serenity", part 2, Mal asked Jayne why he didn't betray him, and Jayne says the price wasn't high enough. In this episode, we see what happens with the price is right: Jayne has no problem selling out Simon and River. What he really doesn't comprehend is the trouble that will get him into with Mal. Of course, we don't know what Jayne's plan was once he had the money - was he going to return to Serenity? Did he really believe Mal would believe Simon and River were somehow caught but he wasn't? Jayne hasn't realized two things yet: first, he's not nearly smart enough to out-smart Mal; second, Mal believes that any insult or harm to the crew has been done to him.
I remember that the first time I watched this episode, I really thought that Mal would let Jayne die. Even with the reprieve Mal has given Jayne, the dynamics between them should be marked colder now. Mal will have to keep an extra eye on Jayne until he's regained the level of trust that he originally had as a paid mercenary.
This episode should mark a turning point for River's condition, which may lead to interesting revelations about the Alliance, if River is able to articulate them. This episode also should be a minor turning point for the situation on Serenity itself, since for the first time that we've seen, the crew has had a major success in getting away with the medicines to sell on the frontier. For awhile, money should not be an issue.