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It's Unification Day (the anniversary of the day the Independents surrendered to the Alliance in the civil war), and we find Mal, Zoe, and Jayne in an Alliance bar, ostensibly looking for a contact for a job. While they succeed in that, Mal also succeeds in egging on an Alliance supporter into picking a fight. The three of them take on the whole bar, but the odds are against them, so they call Wash in in Serenity to whisk them away.
The criminal mastermind with a job for them is Niska. He's well-dressed and well-spoken, but demonstrates to them his ruthlessness about anyone who fails them. He wants them to rob a train.
The plan is that Mal and Zoe will board the train as passengers and sneak into the car with the goods. They will open the roof hatch, and then Jayne will be lowered from Serenity to hook up the goods, and they will all be lifted away. No sweat!
The first complication is when Mal and Zoe discover that one of the train cars is full of Alliance soldiers. Nevertheless, events start out going according to plan. When Jayne is lowered in, some inadvertent loud noises are made, and a soldier comes to check things out. A clever diversion by Zoe keeps the soldier from getting a good look at them. But, only Jayne and the goods are lifted away - after Jayne is shot in the leg - Mal and Zoe retreat back into the passenger compartments.
The theft causes the local police to detain all passengers for questioning. Mal and Zoe overhear the police saying that the stolen goods were urgently needed medicines, making them wish they hadn't been successful. While detained, they pretend to be newlyweds just arrived to look for jobs. While the sheriff questions them, they discover that the medicines are for a degenerative disease that everyone on the world has due to fumes from the mines upon which the world depends.
On Serenity, while Simon tries to tend to Jayne's gunshot wound, Jayne insists that they need to leave Mal and Zoe behind and complete the deal with Niska's men. He won't take no for an answer, and refuses to listen to Wash, Kaylee, and the others about how they can't leave Mal and Zoe. Fortunately, Simon doped Jayne up with a sedative of some kind, which knocks him out. They come up with an alternate plan.
Inara storms into the detention center looking for her "indentured man" and his companion: Mal and Zoe. She berates Mal for trying to steal money from her and fleeing. The locals are awed at the presence of the elegant Companion, and the sheriff releases Mal and Zoe to Inara. They return to the ship, where Mal says that they will be returning the medicines to the locals: the deal with Niska is off, and he'll return Niska's money.
However, Niska's minions have just arrived, wondering why Mal didn't make their rendezvous. They are not happy at Mal reneging on the deal, and so a knife and gunfight ensues. The crew prevails and ties up the henchmen. Mal and Zoe then try to return the medicines covertly, but the sheriff finds them; he lets them go when he realizes that they have honestly had a change of heart about the situation. Frankly, this seems too good to be true.
Mal convinces one of Niska's minions to return Niska's money and tell Niska that they have no hard feelings. Somehow I doubt Niska will feel the same - presumably he had plans for the stolen medicines.
Throughout the episode, River has been having coherent and incoherent spells. During some of her less-cogent rants, she talks about her tormentors as being "two by two, hands of blue". At the end of the episode, we see two agents of some kind, apparently wearing blue gloves, asking questions about River. They are asking Alliance soldiers that never even had contact with Mal, let along River, so it's not clear how they discovered that River was in the vicinity.
This episode was fun for the twists on the traditional western: a maglev train instead of a train on rails, carrying the goods away via spaceship instead of horse, and the loot being medicine instead of money. We get a bit of an idea of what kind of "job" Mal and the crew are willing to do.
The loot turning out to be medicine highlighted two things. First, how desperate the colonists on the periphery of the planetary system are for basic supplies. Second, Mal's someone convoluted honor: sure, he'll rob, but not from the needy. But he's not quite Robin Hood, since he is looking to make a profit. I hope that the money they got from Patience in the previous episode was substantial, because if they keep quitting jobs, it's going to be hard to make ends meet.
Mal has probably made a personal enemy of Niska, which can't be a good thing. Plus, Niska would seem to be in a position of some power and could put out a bad word about Mal, which could hurt them for getting future jobs. I did enjoy Mal "persuading" Niska's henchmen to return Niska's money: when the first guy didn't agree, Mal says darn and pushes him into the ship's engines. Killing someone shouldn't be funny, but the contrast between this action and a typical TV show was amusing - who needs torture or persuasion when you can just kill this guy and work with the next one?
We get more of a look at Mal's personality. First, his tradition of starting a brawl every Unification Day - he clearly hasn't gotten over the surrender of the Browncoats. Next, his glee when he realized they were going to pull off the train robbery right under the noses of the Alliance soldiers. Finally, even with Book's close questioning, he completely evades answering why he allowed Simon and River to stay - I think Book may be right, and the reasons aren't clear to himself. However, I do think that rebelling against the Alliance's wishes is a large part of it.