In the commentary, Joss points out that he wanted to make it absolutely clear to the audience that the heroes might die. Wash's death is consistent with the highly cynical universe. Not only was it subverting Contractual Immortality, but it was also subverting a Crowning Moment Of Awesome.
The significance of the final scene between Mal and River at the end of the movie can take a while to sink in. Specifically, as Mal is telling River about love, she is curling up in the copilot's chair, wrapping her arms around her knees, in a Fetal Position Rebirth - exactly like she had been shown in the very first scene she appeared in in the pilot, except in this case, she's awake, clothed, sitting up, and calmly smiling, while in the pilot she'd been u exactly unconscious, naked, lying down, and awoke screaming. The contrast and the symbolism - that River's struggles in the series and movie have led her to take a hand in her own destiny instead of being a helpless, gibbering wreck, was beautiful and so very subtle
And, for another commentary-inflicted moment: why does River "want to hear" Mal say his piece? Because hearing is what normal people do, instead of reading minds; plus, she's overjoyed to be able to understand without her crazy getting in the way.
Why did learning what happened on Miranda drive River crazy? River didn't just learn of what happend, she felt what happen to every person and it shows how strong River really is that it didn't kill her. Remember that in the series, Simon's exam establishes that River has no emotional filters. Essentially, her problem is the exact opposite of a sociopath's: she has too much empathy. If she were to unwittingly pluck the Miranda secret from a high ranking official's mind — not just hear about it on the news, but be exposed to it, unwillingly, in its totality — it's not hard to imagine that it could overwhelm her mentally and emotionally, especially when you consider the torturous situation she lived in at the time.
Not only does the Alliance avert the typical SciFi Card Carrying Villainy, but they're actually a much greater threat because of it. Anyone with half a brain can see that people like Emperor Palpatine or Grand Moff Tarkin are incredible assholes and should be resisted. And even if they do manage to cow the populace into staying in line, the populace will be exactly that, cowed into staying in line and not deviating from their predefined role when really, in order for a society to prosper, people need to be free to change and evolve. But with a set up like The Alliance, people won't really realize what's going on until after they are affected by it; who cares if some little girl gets her brain cut up as long as its for "The Greater Good" (provided, of course, that it's not their sister getting her brain cut up — but by the time that happens, it'll be too late).
For the whole series, the incentive is to say "Yes, the Alliance was mean to River, and their officers are a little humorless, but their goal is for everyone to live in a shiny democratic utopia free from want, and the Mal's goal is effectively for everyone to live on mudballs ruled by petty dictators and thugs." Then the Big Damn Movie happens, and Miranda strikes everyone as completely in character for the Alliance, and puts things in perspective. In the end, it's not so much about Good vs Evil as it Law vs Chaos.
An in-production version, as well: Joss and Gina Torres are talking about Zoe's talk with Mal during the ending scenes, and one of them mentions how Zoe's summation of Serenity's status applies to her as well. Nathan overhears this and wonders audibly how he managed to miss that one...
A solo River taking down an entire army of Reavers (who don't even have the disadvantage of fear, or of hesitance at attacking a little girl) seemed a little unrealistic (if awesome) even for her. Then the Alliance arrives direct through the wall and makes the backdrop even more campy. It took me a few viewings to realize the connection: River won partially because the Reavers who hadn't gotten in the room yet were suddenly attacked from behind by the approaching Alliance troops, splitting their attention.
The Reavers are a result of an Alliance experiment to create a perfect world gone horribly right; River is the result of an Alliance experiment to create a perfect soldier to fight the Reavers gone horribly right. The Alliance just will not learn their lesson, will they?
The Alliance wanted a world perfectly at peace? They got one. They wanted a psychic commando? They got one of those, too. Even the Reavers can be seen as 'without sin'. There are no criminals among them, no coercion, even. Every last one of them is a perfect manifestation of their inherent nature, as innocent as a scorpion. They are not evil, which was exactly what the Alliance was hoping for. The twist is that they are also simply too dangerous to be allowed to exist. All of this ultimately validates Mal's warning: "...sure as I know anything, I know this: they will try again." The experiments on River as well as Miranda are proof that they will continue to try to make people better. They will not stop.
The Operative: A lot of innocent people are being killed in the air right now. Mal: You have no idea how true that is.
River's powers and Simon's knowledge:
First viewing: Wait - Simon knew all along that River was designed to be a mind-reading assassin? But he played dumb during the series, even when the crew's life might depend on it. What an outrageous retcon! Also, it's completely out of character for Mal to abandon Simon and River. Second viewing: Oh, so that's what was eating Mal about the Tams....
In fact, this is an important bone of contention later on after River rips apart the bar. Mal gets pissed at Simon because he wasn't telling them everything he knew about River's conditioning, and it really comes out when he confronts Simon after the brawl.
The series itself takes on a very interesting new light if you go through it with the mindset that Simon was fully aware that River was a psychic but that he was trying to hide it from the others. Every time he talks about River and her "awareness" he seems confused and hesitant and uncertain - not because he doesn't know what happened to her, but that he is aware of what happened and that he's trying to keep a lid on it and not sure how to do so.
This is most obvious in Safe, where it's clear he's not surprised River knows things about the mute girl she can't, but rather he's trying to find an explanation other than "my sister is psychic."
At the end, River is shown both doing some electrical repairs on the ship and taking over Wash's role as pilot, skills she didn't show prior in the movie. Except that A) she's a genius who takes to difficult subjects like anyone else does to breathing, B) she's living on a ship with a genius mechanic and a genius pilot, and C) she's psychic. It would be ridiculous if she didn't pick up some skills from Wash and Kaylee. What's she pick up from Mal and Simon? Being a Determinator.
After River's programming was triggered, and then Mal and Zoe are trying to decide what to do with her, knowing she's dangerous? Well, right after that, River has a conversation with Simon (sort of) where she says "They're afraid of me. Well, I'll show them. Oh, God." She is not referring to the crew of Serenity alone - she's also referring to the Alliance, who are becoming desperate to capture of eliminate her before she reveals their secrets. Talk about powerful dialogue with multiple meanings.
The Unification War:
The entire war between the Alliance and the Browncoats wasn't about simply becoming a 'monopoly' in the 'Verse. (After all, with better medicines alone, the Alliance could have launched a 'hearts and minds' offensive with their better technology). What, then? Miranda had become a launching point for an entire fleet of Reavers. From at least one instance, there's reason to suspect that it might "catch" (ie, the Stockholm Syndrome making that one guy 'join'). If they left the Independent worlds be, they'd stay free but also disorganized—and either die piecemeal or actually provide 'reinforcements' for their push on to the Core Worlds. Someone in command simply found a pretext to take action. Probably not out of loving concern for the outer worlds, but out of a sense of self-preservation.
This is even more plausible when you consider their motive to suppress the information. If the outer worlds are free, then it seems likely that sooner or later someone is going to try to find out the source of the reavers, and hunt down why they just popped up out of the blue, possibly starting with the planet that mysteriously died off just before they showed up. If they're in control of the outer planets, even nominal control, they can prevent that from happening. AND, the war likely served as a major distraction from any public attention to, or investigation of, Miranda. In peacetime, a terraforming failure might be notable enough to attract attention; with a war on, it would almost certainly be ignored.
You would think that after all The Operative has done to Mal and his crew, he would have earned himself the mother of all gruesome deaths, like being fed feet-first to the Reavers or something. Mal sparing The Operative's life seems like another of Whedon's many subverted tropes, namely in this case how the good guy always has to kill the bad guy. Okay, Mal showed him the truth about the Alliance, but was that really worse than killing him, really? Acomplete loss of faith really was the worst thing Mal could think to inflict on someone. Because he would know, he suffered the exact same thing at Serenity Valley. There's a deleted scene that makes this more explicit, where the Operative asks Mal how he was able to keep going after Serenity.
When the Operative asks Mal what his sin is, Mal replies "Hell, I'm a fan of all seven. But right now, I'm gonna have to go with wrath." This seems like a snarky Pre Ass Kicking One Liner—which is probably what Mal intended it to be—but if you think about it, wrath really is Mal's sin. Most of his actions in the movie were motivated by anger, first at Book's death and then at the knowledge that the Alliance had wiped out an entire planet and created the Reavers attempting to make people "better". Even in the series, while Mal has mostly resigned himself to the Browncoat's defeat, he still hates the Alliance (and depending on your interpretation of his faith, God) for the war. Had Mal not cut him off, "wrath" is what the Operative would have told him.
It's a little thing, but watch the Operative's reaction when Mr Universe's fembot says "Mal?" The first thing he does is to look around him, because he doesn't know it's a recording, but thinks she's actually addressing Mal.
During the heist at the beginning, when Zoe stops the 'hero' from drawing his weapon, she tells him that a hero is "a person who gets a lot of people killed." At first, it seems like a random one-liner and it's a pretty funny line, but it also applies to the rest of the movie: Malcolm Reynolds plays hero by resisting the Alliance and gets a whole lot of people killed as a result. Maybe Zoe should've saved that piece of advice for her own captain.
The Operative goes on about the fact that Mal is “not the plucky hero, the Alliance is not an evil empire, etc.” He promptly gets royally pwned because he forgot that Inara is not the damsel in distress.
The point of her praying. It lets her hide what she's really doing, which is bracing herself for when the flashbang goes off.
As for why she would just happen to have a disguised flashbang? As Atherton Wing taught us, not all men who can hire a Companion are strictly civilized, so Companions must have discrete tools that they can use to protect themselves. Which ties in with Inara's earlier complaints (possibly from a deleted scene) about how the girls in the training house are not ready for the dangers of the 'verse that their line of work can bring them, thinking that being a Companion is all wealthy men and romance. Even odds if this makes her The Last DJ as she seems to worry about, or merely a Veteran Instructor that the Guild is hoping will help prepare their students.
The reavers are a dark parallel to the "Indian Savage" trope. A foreign horde, impossible to reason with, that descends on civilization without warning, does horrific things, and leaves without a word.
In a deleted scene at the end of the movie, the Operative makes the parallels between him and Mal obvious by asking Mal how he was able to keep living after the battle of Serenity Valley. Mal's response is "If you're still standing there when that engine starts, you never will figure it out." This sounds like a simple threat, but it's actually the answer to his question - the only way to go on is to "keep flying," not to let yourself get stuck.
The last line during the death scene of Shepherd Book is frequently misquoted. The subtitles don't include the word 'her' but are otherwise word for word reproduced here.
Book River! (Who isn't there) Mal (To Doc) C'mon! (To Book) Hey! Book (Continuing)I don't care what you believe, just believe in... her.. Whatever sh...
A couple small ones from dialogue. After they fled the Reaver attack in town, Zoe told Mal that they never would have left a man stranded in a time of war. Mal replies that maybe that's why they lost. Later on, after River attacks the bar, they all flee on board the ship. Jayne asks why they didn't leave Simon and River behind. Zoe and gives the Captain a significant glance. Another one happens between Mal and Inara. Soon after the first fight with the Operative, Inara is arguing with Mal, telling him this fight isn't the war and that she's too many versions of him to know who she's dealing with. Mal tells her that if he starts fighting a war, he guarantees she'll see something new. After the Operative kills Book's colony, Mal goes to war and Inara is shocked (along with everyone else) when he starts ordering the bodies strapped to the ship. The entire movie, from start to finish, is Mal moving to a war footing.
You know that little spin at the end of the film? It's a pirouette. River made Serenity dance.
Always wondered who opened the blast doors after River killed all the Reavers on Mr. Universe's planet, when she was standing in the middle of the bodies, holding two weapons? Mal had just come up from the lift and the doors opened about 20 seconds later, roughly the time someone would walk between the top of the lift and the doors. They were still on automatic (from the inside).
When Inara waves Mal and he brings up the trunk she forgot, they both quickly say, "I didn't mean to leave any stuff" and "I didn't look through the stuff," they're both lying. Mal did look through Inara's things, because it was all there was left of her, and Inara intentionally left the suitcase there just in case she ever needed an excuse to call Mal. This is also the reason why it was so conspicuous that they didn't fight. Ordinarily, Mal would have instantly begun snarking about the leftover luggage if he didn't suspect something was wrong, and Inara would've gotten angry that he looked if she wasn't warning him about the trap The Operative was setting for him. In this case, what's not being said is the real code they're using.
When the tape is broadcast at the end, it goes to every single receiver in the galaxy. Think how many young kids must've been innocently watching tv and suddenly they see a woman being horribly raped to death instead.
Some subtle references: Not for nothing is the name Miranda used. Some of the bulkheads on the Alliance ship are more explicit: C-57D. And what are the reavers, but monsters from the id? O brave new world, that hath such people in it...
Word ofGina Torres says that Zoe was pregnant during Serenity. And then come the questions: Did Zoe know? If she did, did she get around to telling Wash? Did Wash die knowing that he would never see his child, or did he die without the knowledge that said child even existed? You're welcome.
As Serenity makes its way through Reaver territory, Mal tells Wash to turn off the intercom to spare the crew from hearing the agonized screams of the Reaver victims. One crewmember, however, cannot only still hear the screaming, but can feel the reasons they're screaming.
A small one: after the bar beatdown, River is very upset at the idea that Simon might put her to sleep again. Now remember the scientist at the beginning saying that most of her mental conditioning was done in her sleep, and that the Alliance would probably want that to happen when it was convenient for them rather than her, and the reason for the "safeword" might not be what Simon thought.
The end of the heist at the beginning, after they take off in the hovercraft. Leaving a man behind because there would be too much weight on the craft, and a speedy getaway was needed? And they picked throwing him off as opposed to dumping the cargo? It's rather reminiscent of the events prior to "Jaynestown", isn't it?