As I was watching it I had a pen and paper beside me, jotting down my thoughts, things that made me laugh, continuity mistakes that annoyed me and the rubbish explanations they used to handwave them away ("I don't like to remember squints cos they're flaky on the witness stand and therefore all three of us will conveniently forget this meeting ever happened come The Man in the Morgue.") but the end of the episode depressed me so much that I don't really have the energy to go through my notes and make any kind of sensible reaction post.
So instead you get my rambling thoughts as I try to work out my feelings towards the end of the episode...
I can kinda see the argument that Brennan's reaction was in character for her, but I'm not entirely convinced of that. She has made so much progress through these years and while I wouldn't expect them to immediately jump into bed together I would have thought she could have given them a chance.
And as a shipper this bothers me because it's just not how these things are supposed to go. (Yes, I realise how ridiculous that sounds but I'm struggling to think of a better way to express it.) You watch these characters who obviously belong together dance around each other and it's ok because you're confident that it's leading up to something and once they admit their feelings for each other they'll be together.
I suppose what worries me is that they're going to try and drag this out even longer. I love shipping but I also love seeing the characters together and watching how their relationship fits into the context of the show and all the elements it introduces. So I really don't like it when writers deliberately keep couples apart for longer than makes sense. I know a lot of people think that couples getting together ruins the show but I think keeping couples apart for too long ruins it more. Eventually it becomes ridiculous and you just stop caring. Or the methods used to keep them apart ruin the characters and whatever relationship they already have.
What I am clinging on to though is that it showed how important Booth is to Brennan. She cares about him too much to risk hurting him and she doesn't want to lose him from her life. She didn't reject him because she doesn't love him, she did it because she loves him too much.
There's also a not-so-small part of me that's hoping this is some kind of misdirection. They make us think that there's no hope for these characters, at least not any time soon, so we're not expecting it when something happens in a few episodes that brings them together. (I'm completely unspoiled so this is all just my wishful thinking.)
Finally, I've often thought that Vienna Teng's I Don't Feel So Well fits Brennan in many ways and it's pretty much all I could think about while watching the final scene.