The Twist in the Twister
A varied version of a typical Booth/Bones struggle: he wants to help her, she insists she can do it on her own. But the fact that she's pregnant with his baby pushes them both further in their positions: he's even more vigilant about helping her, this time helping her get up, and she's more insistent about getting herself up, mostly because of his increased insistence at helping her but also, I'd speculate, that she wants to prove she can manage being pregnant on her own, not having anything to do with Booth but rather because she's so used to being self-sufficient. She was planning on doing it on her own just a few years ago, after all.
Then the conversation starting with the ramen. He insists she shouldn't eat it, but she's already planned it out – she'll have a low-sodium dinner to counteract it, further showing her self-sufficiency. She goes on to accuse him of his overprotectiveness in a logical, rational, reasonable fashion, partly because it is true – of course he's being overprotective, he's overprotective with her more often than not when she's NOT pregnant, so with her being pregnant with his child of course he's going to be over-overprotective. Even when he's trying to say he's not overprotective, he gets another overprotective comment in there. But she's partly doing it to legitimize her dedication to her self-sufficiency.
And she gets even more dedicated once she realizes he lied, which she reacts to by risking getting attacked by the storm just to prove she can get through it unharmed and show him his lying was in vain (and tried to punish him for it even more when he still insists she shouldn't have come after the tornado, when she leaves him at the site after he's seen his car is destroyed).
Which she connects back to the self-sufficiency once he gets home, except we learn it's actually more than that - “you think you have the right to control me because I'm carrying her protege”. I'd go so far as to say it has more to do with her just believing in her self-sufficiency, it connects reasons for her not wanting to have marriage or long-term commitment – she's afraid it'll result in someone wanting to control her or change her. With her being pregnant, the idea of long-term commitment is a constant presence now, and it was something she insisted she would never be involved with for all of her adult life. No matter what the situation now or how much she's changed, it is still frightening to have something you've fought against for so long suddenly become a likelihood. Mindsets can change much more easily than behaviors resulting from those mindsets, and the longer the mindset has been in place, the more ingrained the behaviors are. So she finds every chance to highlight Booth's overprotectiveness and her own ability to be self-sufficient.
And, the final scene. He knows her, he knows she's not going to let up, so he has two options: either stop being overprotective, or give her a logically laid-out explanation as to why he does this. Note “logically laid-out”, not “logical”, because the level of his overprotectiveness is not “logical”, at least in her eyes. But she needs to know he's not doing it because of any fault of hers, as she's made it out to seem so far. It's not because he doesn't trust her, because he doesn't think she can manage on her own, because he wants to control her – it's that he feels better protecting her and their child in the albeit small, minute ways he can, because he won't always be able to be. Despite it being a logically laid-out argument, she doesn't buy it as such, but again, you can't really expect her to accept it on any level because she still has that deeply-ingrained behavior in place. But when he points out she has a little bit of crazy too, he is completely correct – I mean, she risked being injured or killed in that storm just to prove she could manage it despite Booth's lie. Yes, she says its because she wanted to talk to the chasers and it made her think of things she wouldn't have thought of otherwise, but also she could have simply asked to arrange an interview after the storm, or even talked over the phone later on. She too has her own delusions, in this case her dedication to unnecessary levels of self-sufficiency, but unlike Booth, the one still more understanding of the emotional/psychological aspects of himself and their relationship (after a bit of stubbornness and pushing it away, as always) despite how much she's grown, she won't always be able to be as understanding of them, especially while it is still happening and she uses her rationality as the deflector.