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Serenity comes upon a derelict ship. Wash and Mal deduce it is some kind of cargo ship retrofitted to transport settlers to the outlying worlds. It's not immediately obvious why the ship is derelict, and Mal decides they should explore it to see if anything valuable has been left behind. Even though no one directly states it, it's clear that things are a little off; River claims that she hears ghosts screaming. Serenity docks with the derelict.
Mal and Zoe do the initial reconnaissance of the derelict ship. They find that whatever happened to the passengers was very sudden, as meals are still on the table. There is no initial sign of bodies, survivors, or struggle. The lifeboat is gone, although as Zoe notes, it couldn't have held as many settlers as were likely on the ship. The ship's atmosphere is viable.
Mal calls Kaylee and Jayne to come over and help search for valuable items to scavenge. Jayne pulls a practical joke on Simon, getting him to suit up unnecessarily, playing on Simon's fear of the vacuum. Once he's there, Mal teams him up with Kaylee to search the ship; Kaylee and Simon begin ransacking the engine room. Jayne heads to the mess (?), while Mal and Zoe head to a storage area that is the most likely location of any useful supplies.
The atmosphere while the crew is exploring the derelict is pretty creepy, since the lights are out and it's a mystery about where everyone went. This is amplified when River decides to wander onto the derelict - it's always so strange to see her walking around spaceships in her bare feet. She is drawn to where Mal and Zoe are. She enters the storage area and looks up; this causes Mal to realize that the passengers have not left - their bodies are suspended from the ceiling in various stages of mutilation.
Mal knows that only reavers could have done this, and as always, the thought of reavers puts everyone into high gear to get as far away from their works as possible. Mal orders everyone off the derelict. Just as he does so, Jayne is attacked by a survivor in the mess. Mal and the others help him corner the survivor, whom Mal knocks unconscious and they take back to Serenity.
On Serenity, Simon examines the survivor and finds that he's essentially fine, just malnourished; Mal orders him to be knocked unconscious again. Later, Mal and the crew discuss their next course of action. Mal and Jayne want to disconnect from the derelict and take off; Book argues for staying long enough to take down the bodies and have some kind of funeral service for them. Surprisingly, Mal agrees to this without too much argument: he assigns Book, Simon, and Jayne to the task. Inara is tasked with supervising River to make sure she doesn't do any more wandering.
Shortly we see that Mal has an ulterior motive for agreeing - he wants to keep everyone busy while he, Zoe, Wash, and Kaylee find and disable the reaver booby-trap he suspects activated when they docked. The directing in this sequence is effective at building suspense and keeping things moving. We cut between scenes of Kaylee disabling the booby trap, Book and the others attending to the bodies, the survivor awakening and finding a knife, and River somehow feeling some of the survivor's tortured emotions (although no one else realizes what's happening). When the survivor took the knife, I was expecting him to escape from the infirmary and attack, but it never happened.
All of the tasks are finished and the crew is secreting their scavenged goods in the hidden cargo compartments when an Alliance ship shows up. Mal quickly has all their "loot" put out in plain sight, and despite Simon's apprehensions, comes up with a plan to hide him and River. This is some nice misdirection, because we are led to believe they are hidden in the cargo compartments, and then when the Alliance Captain says he's familiar with the hidden areas in firefly ships, we worry. Not to fear, as Simon and River are hiding in spacesuits outside Serenity - again, a good exploitation of Simon's fear, which is nicely contrasted with River's child-like wonder at seeing space up close.
The Alliance captain concludes from the circumstances that Serenity's crew is responsible for the deaths of the derelict passengers and that they were motivated by the opportunity to ransack the settlers' supplies. All of the crew are taken onto the Alliance ship for interviews.
The interviews themselves are small windows into the characters. Jayne refuses to say anything. Zoe answers as shortly as possible and refuses to directly answer most inquiries, even about her husband, saying they are very private. Of course, Wash has no problem talking all about what's so great about Zoe and their relationship. Kaylee natters on about engines. Inara is very politely interviewed. When the captain interviews Mal, we see that he has done his homework and knows about Mal fighting in Serenity Vally during the civil war. In the end, the captain's conclusions aren't changes: he says that Mal's ship and possessions will be auctioned off and the proceeds used to pay for his defense.
Mal tries to tell the captain the true story, but the captain is green and doesn't believe in reavers. When Mal says the survivor will support his story, he learns that when the Alliance soldiers found the survivor, he had used the knife to split his tongue in two - the captain thinks Mal tortured him. Mal realizes that the survivor's behavior is the horrible legacy of the reavers: the survivor saw the reavers do such awful things that he has basically decided the reavers' way of life must be superior, so he has decided to emulate him. Mal fails to convince the captain, until the Alliance crew brings the captain the news that the survivor has murdered the medical staff and fled.
This gets the captain's attention. He decides to let Mal take the lead in finding the survivor. Mal realizes that he will flee to Serenity to plan, and sure enough, we see him hiding in the common area. The captain will not unhandcuff Mal, so Mal must lead the way completely vulnerable. The survivor, now self-pierced and mutilated all over his face, attacks the captain, but Mal strangles the survivor with his handcuffs.
In short order, Mal and his crew are released and Serenity is free to go (sans their loot from the derelict). The captain takes Mal's advice and destroys the derelict.
This episode did a good job of being extremely creepy, with the mystery of the derelict passengers, and then the thought of them all being tortured and killed, and then the horrible change in the survivor. The Alliance ship showing up and completely mis-reading the situation was the cap to the situation.
The reavers are obviously completely awful beings - as Mal says, they aren't human any longer. It's not clear what some of their motivations were in their actions. Mal says they kept the survivor to watch them do their awful deeds. I can understand that - but then why leave him behind, instead of killing him or taking him along as a future witness? Did they leave the booby-trap on the derelict with some way of notifying them if it had been activated? Why didn't the reavers take some of the food and supplies that Mal's crew scavenged? Of course, reavers aren't really sane, so I guess one can't expect them to act rationally.
The Alliance captain was unexpectedly not stereotypical. Despite Mal's prejudices against the Alliance, the captain was neither arrogant enough nor stubborn enough to refuse the good sense Mal presented him. He also was not extremely bound to the letter of the law - even when he discovered the truth of the situation, it was still probably the case that Mal violated some laws in looting the derelict ship instead of reporting it; he realized that Mal's saving of his life merited some leniency.