I thought this was a good one to end a season (as opposed to a series) on, despite that it's far more powerful when you don't know what's coming. But, I guess being tired, I only feel like mentioning trivial details.
There's another hint (two actually) that Book is himself a potentially dangerous individual with a secret past. I hope to read the comic one day that is supposed to expand on his backstory.
A detail I THINK I saw is in the early 12th minute mark, between when Simon asks Kaylee if she doesn't see River as a person, the scene going down to show River balancing on rails, apparently paying attention to the meeting above. As the view went between decks (transitioning scenes) it really looked like there was an alien bug (antenna and wings twitching). If I'm seeing it right, it was a nice if trivial easter egg. It would make sense that such would happen. (And adds to Kaylee soon after telling Simon, "Don't let the space bugs bite!" And then kicking herself for saying it, but maybe it really was something to worry about.)
Another trivial detail, River again repeats what was said to her earlier with "No touching guns."
I'll end by saying I'd be so annoyed if even in deep space there were still home intruders.