In Which She Accepts His System

Season 5, Episode 9

The Gamer in the Grease

BRENNAN: There’s a flaw in your reasoning.  I believe that due to my superior learning curve, I can beat you at this game – despite your superlative strength and your remarkable reflexes.  (She hits the buttons on the machine a few times) How do I start the game?
BOOTH: What’s the flaw in my reasoning?
BRENNAN: Dougie Seeger is autistic.  He didn’t care.  His heart wasn’t broken.

BOOTH: So, the dad loved him twice as much.  All right, you don’t like the reasoning and my math.

BRENNAN: I’ve realized recently that you use a different number system, like the Babylonians which was base 60.  I don’t understand your system but I can see that it works. 

After she says “There's a flaw in your reasoning”, he gets this look on his face. The whole conversation thus far has been a typical Booth and Brennan debate. He normally gets frustrated that he can't get her to understand him. In this case, it's not so much frustrated as... disparaging, in a sense. Considering what we know happens six episodes from now, it's safe to speculate that this is not just his usual frustration with her not understanding him, but that it's also acting as a sort of example, in his mind. He's trying to find the right time to tell her that he loves her, and this gets him thinking “well, if I can't get her to understand me now, will I ever get her to understand me? How can the two of us ever work if we think so differently?” etc. etc.

But then, she turns it around on him. She basically says that although she doesn't understand his way of thinking, she sees that it works. She accepts that it works. And honestly, that is the best way they could work as a couple, because I think if Bones were able to completely understand his way of thinking all the time... she wouldn't be Bones. But for her to accept that his way of thinking works, is the best way they can make it in the end. If that makes any sense.