It's hardly the first time Booth's been shot at. It's not even the first time that Sweets has been there with him. But as they go down, Booth instinctively making sure that Sweets is between him and the wall, he feels a swooping fear in the pit of his stomach that, later, he finds difficult to ignore.
Here's the thing: whatever crazy deductions Sweets and Gordon Gordon and the assorted other FBI shrinks have made about him in the past, Booth is not averse to, y'know, having meaningful relationships with people. Caring about them, all that. He's got Parker, for one, and fine, his relationship with Rebecca crashed and burned long ago, but it was a good thing for a while. There's Bones, obviously. Pops and Jared, and, yeah, there's some tension, but there's his mom. And Cam, and Caroline, and he's got buddies from his Ranger days and friends in the FBI – he's not an island, OK?
He just really didn't expect that one of the people he would care about would be Lance Sweets, FBI psychologist wunderkind.
And frankly, Booth's not even sure how that came about, because the kid pushed all his buttons when they first met, and is, even now, way more squint than FBI. Well, maybe that's not fair. Sweets is a nice guy. He's stupidly enthusiastic about stupid things. He wants to help people. He makes a good partner. He's no Bones, but no-one is, so. He'd say it was being forced to live with the kid all that time, but who is he kidding, he wouldn't have invited him if he wasn't already, y'know, fond of him. If he hadn't felt sorry for him, or worried about him, or whatever, lying there in his office, all pathetic and miserable and homeless.
He worries about Sweets a lot, actually. More than he is willing to admit. Or willing to admit at all, really, because Sweets is a grown man and a colleague. But he can be kinda naïve sometimes, and sensitive about stuff, and breaking up with Daisy – the way he broke up with Daisy – really knocked him sideways. Pelant didn't help. Booth wishes Sweets hadn't been involved the way he had. Not the nearly getting shot thing (he's not even going to think about how that could have gone differently, all right? It was all fine in the end), but the way Pelant had used Sweets' work against them; used Sweets. And, OK, shrink juice and Booth's bath tub not being his own and psychology books cluttering up the place, but at least Booth could keep an eye on him at home. Now Sweets is left to his own devices, to go and think about giving up the FBI, roaming wild and free, and Booth is just grateful at this point that he's down as the kid's emergency contact.
Sweets is a good man. And Booth worries about him because, OK, he cares, but he knows that Sweets has sense (mostly) and good judgment and can choose his own path in life and Booth might not be crazy about that but he'll support him because, y'know, he's like family. Sweets is like family to him. Not like a brother exactly – he's got Jared, and it's different – and not like a son – he's got Parker, and it's different – but maybe something in between? Something else? Whatever, Booth doesn't know exactly, and it doesn't really matter. He doesn't have to label it, he's not a shrink. He loves Sweets. There, he admits it. Everyone happy?
Later, in the Founding Fathers, he jokes and says Sweets is like the little brother he never wanted, which is obviously untrue because he has a little brother and he (mostly) always wanted him. But Booth knows people and he knows that Sweets knows that Booth cares, and what do words matter, right? Booth has Sweets' back. He's patted him on the shoulder with an open palm many a time (learned that lesson long ago). On more than one occasion he's mom-armed him in the car when he's had to brake suddenly. Booth has trusted Sweets in his home, trusted him with his kids, trusted him with his Captain America underpants. He's watched kung-fu films with him. He's saved his life. One time (never spoken of since), he woke Sweets from a nightmare and sat with him on Parker's bed until he stopped shaking and automatically ruffled his hair as he stood up to leave.
In the end, Sweets doesn't leave the FBI. He's no less stupidly enthusiastic about stupid things, and no less squinty, and Booth, in his heart of hearts, wouldn't have him any other way.