I thought about this line from Alyssa on a recent episode of Bones:
The show made a much bigger deal of those coping mechanisms and the characters ultimate concern for the humanity of the victims in earlier seasons, but I suppose that point being sufficiently established, they've kind of moved on from it.
…while watching last night's episode.
The episode, in which the show picks up the story of the sniper who brutally murdered the Gravedigger, gets the show back to making "a much bigger deal" about how the characters cope with all the death around them. Because we are starting to see the emotional fallout of the Gravedigger's brutal murder.
Since the Gravedigger's killer, Broadsky, is a sniper that was Booth's mentor, the show has just the right opportunity to explore the sheer brutality of the world in which the characters live and how they cope with it. The episode does a tremendous job of exploring more deeply how conflicted Booth really is about the life that he led as a sniper.
Booth has always been the most conventionally moral character on the show. He's a man who believes in the rule of law and religion and morality, but he's also a man whose job for quite some time was to murder people – and he was very very good at it. Clearly, he was in some denial about what that means. So it makes sense that an off-hand comment from Brennan about the relative nature of good and evil would send him spiralling.
Bones is at its best when Booth and Brennan's worldviews collide**. Because they are in love they take seriously – and to heart – the way the other sees the world. The show has always suggested that Brennan gets more out of this swap than Booth, but that's only true if you already think that Booth's views are more right than Brennan's. In reality, it is equally (if not more) interesting to see how Brennan's more relativistic outlook influences Booth.
Particularly, because nobody on television does vulnerability and self-reflection better than David Boreanaz.
*Not to mention the "actually you two have many similarities" comment. Emily Deschanel delivers those lines so beautifully. I felt Booth wince.
**And similarly, when Angela and Hodgins' worldviews collide. The B-story with the always-fun Billy Gibbons was equally as fascinating.