He thinks about missed opportunities mostly, those small slivers of time that could change everything. There's a difference between missed opportunities and regrets. Regrets are things that you wished you had done. Missed opportunities, well they're a bit more complicated than that. They are the things that could change your life, and maybe not for the better. Everyone has a huge stack of them that they think about. His stack revolves around one person. He knows that most of his missed opportunities don't have to do with Temperance Brennan, and he certainly does not regret any of his actions or dealings concerning her, yet it is her that dominates his thoughts.
All of the missed opportunities he's had with her spread over his brains like small roads that lead to unknown and dangerous places. He doesn't go to these places often, but every once in a while he allows himself to take a walk down one of the roads. There are many opportunities with her, too many to count at this point, but there are several that he favors. These are the roads that he can't qualify. Some are bordering on regrets, and the others he is happy he didn't take. He's not sure which one of these thoughts is more dangerous, because they both lead to the same conclusion. He always stops before he arrives there though.
There are the simpler ones like he could have not stopped her at the airport. It was not his decision on whether or not to involve her, but when he explained to Cullen that she had blocked his contact with her and that the last time had not gone well the deputy director understood. This understanding could have stopped it. Yes, the FBI's forensic team wasn't as advanced as the Jeffersonian squints, but they could have managed. It took him an hour sitting on a park bench with an already cold cup of coffee to decide whether or not he should keep trying. In the end he had remembered that a guy in Homeland security owed him a favor and he couldn't help but want to see the look on her face when he "rescued" her from them. He didn't have to though. He could have put away the cell phone, downed the coffee, and left it at that. Then he wouldn't have to put up with her scientific crap, her insensitivity towards victims, and her disdain for his job. But if he had done this they wouldn't be partners and there's something about this thought that makes him feel a bit sick.
It could have just been sex. He knows that sounds crude and odd considering their relationship now, but there was a time when it could have just been sex. He has never and will never admit to anyone that he was incredibly attracted to her the first time they met. Of course, that was before she spoke. She immediately told him he was late in meeting her, she did not have a lot of time, and that she resented the fact that the FBI thought they could just use her whenever they wanted. Twenty minutes after that was the first time he called her "Bones" and she gave him such a look of hatred that he knew he had selected her new nickname. He wasn't an idiot and knew that there was enough sexual tension between them that it would be so easy to just give into it. If they had he could have just slept with her and never seen her again, gone on with his life without ever thinking of her except for when he saw her on TV for her book.
There was a chance where they could have slept together and still worked together. This road is not so different from the "just sex" road, only it included them still functioning around each other. This road also has an exact moment, the moment where she told him to "be a cop". He could have kissed her then, her back up against the wall and his hand next to her head. Part of him desperately wanted to, and he still isn't sure what made him not. He knows how it would have gone though. They would have had sex, ignored each other for a few weeks, he would be assigned to a case with her, and they would pretend it never happened. Of course Angela would be pushing her to go on a date with him, and she would drop hints to him about how pretty Bones looked that day or what a cute couple they would make. But he knows that if it had happened like that it would never happen again. He's not sure how he knows this, but he's completely sure of it and part of him is happy that it didn't happen then because of that.
There was an opportunity for them to just be partners. If he is honest with himself he knows that they were never just partners, but he knows when he crossed the line. They had just gotten to the point where there was trust and had moved away from everyone waiting for them to get together. It was a descent partnership and he could have left it at that. Then there was a hit put out on her. The smart thing to do would have been to tell someone, anyone. It would have been dealt with; it was not like the FBI did not have procedure for this. Instead, he shoved his gun into the man's mouth and swore that he would kill him. In retrospect this was not exactly the smartest way to deal with it, but it solved the problem. This was when the line was crossed, when their partnership changed.
It was only weeks later when the opportunity to date her came. They were in his hospital room and she canceled her date to stay with him. They sat in his room eating pudding and watching TV for hours before the nurse kicked her out. She came in and said that visiting hours were long over and unless this was his wife or girlfriend she was going to have to leave. They had looked at each other for a minute and the words "girlfriend" formed in his mouth before she apologized to the nurse and hurried out of the room. When he thinks about this he is almost sure that it would have ended as soon as it had started. They would have dated for maybe a month before fighting over something stupid and breaking up. He would make an excuse about why he couldn't work with the Jeffersonian and she would go on one of her post-breakup trips. That would be the end of it.
When he tells her about one of his missions it is the first he thinks that maybe they could have a meaningful and lasting relationship. He's never considered telling her until Hank told him he should. Of course, Hank also mistook Bones for his girlfriend, but he doesn't like to think about that. He doesn't talk about these things with anyone and to tell her feels like he's allowing rocks to fall of his back. She listens though, and doesn't even make a comment about it. Her grip on his hand is tight and he squeezes her hand just as hard while he relates his past. She doesn't judge and they just sit there for a while. When they finally do leave she doesn't let go of his hand until they are halfway to the car. He could have kept holding her hand and maybe that would have led to something more.
They find her mother and everything he thinks about their partnership goes away. Suddenly the only thing he thinks about is finding whoever did this to her and her family. He wants the bastards to pay more than anything else, because when he looks at her like this it makes his heart tighten. He shows up at her door with Chinese food and tries to assure her that someone cares about her without actually saying the words. He has never seen her look lost and he finds that this scares him most of all. He swears to himself that he will never let her be lost or forgotten. His head knows that this is not the time to start a relationship, that she is messed up and confused. Looking back on it though, these reasons seem more like excuses.
She goes to visit her brother and Cam comes back. These two things don't happen together, but somehow they change everything at the exact same time. They haven't drifted apart, but the finding of her mother has made her put up her guard even more. She trusts him, but things have changed. He finds himself looking at Cam and wondering what it would be like to try it again. He hasn't had a relationship or sex since Tessa broke up with him and now there is a beautiful woman in front of him who is still interested. Things are rocky at first, she threatens to fire Bones, but soon she finds her place amongst the group. By no means is she their equal and maybe including her in their small "family" doesn't quite work, but she has a place. He isn't quite sure how they began sleeping together again, but it works. There are opportunities that come and go, but he is with Cam and he is not a cheater, at least not in the traditional sense.
Her father came back yesterday. He came back and her world got flipped around again. Things like this should not happen to people like her. These horrible, horrible things that just knock her feet right out from under her each time she has good footing. He does not let her leave his sight and as soon as she does he knows she's in danger. Her father looks him dead in the eye and tells him to take care of her and that is when he knows he won't stop him from leaving. He's been given the "protect my daughter" talk from the fathers of many girlfriends, but this time is different. Her father is almost giving her to him. This sounds somewhat barbaric and it is not that he sees her as property, but he feels like Max Keenan is letting his daughter go and allowing him to be the one to look after her. His mind flashes to weddings and the fathers giving their daughters away, but he cannot think of things of this nature and her.
After the craziness he stands outside the diner with her. His hand rests on her chin and she is looking at him in a way that makes his head spin. This moment is an opportunity; he can feel it all around him. Normally he doesn't realize that it is an opportunity until it has already happened, but this one he knows. He leans forward a little bit and thoughts of Cam and partnership swirl in his head. She is standing in front of him and he realizes that if they really wanted it they could make it work. Then Zach taps on the glass. The hazy world snaps back into focus and they both offer up smiles as a sort of apology. She makes a crack about squints and instructs him on how to congratulate Zach, but he doesn't hear her. He is lost in the roads of missed opportunities.