A/N: This story follows the structure of season 1, so we're now at episode 2 ("The Man in the SUV"), and things will proceed like they did in canon. Only, not quite ;-)
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The acrid stench of smoke and burned flesh isn't the only thing that makes Booth's stomach clench while he waits for the Jeffersonian team to arrive at the scene of the bombing; he's doing his best not to let on how nervous he is, but he has no idea how things are going to be between them once she shows up. The last time he found himself in a morning-after situation with her, things blew up in his face in a way that led to thirteen months of radio silence, and he isn't convinced that they're going to fare any better this time.
It turns out that he needn't have worried. She bursts onto the scene like a queen taking possession of her realm, but she acts like everything is perfectly normal between them, and even though he knows he should be relieved, he feels just the tiniest bit irked by her cool professionalism. Still, she gets the job done, and Booth follows her around carrying plastic bags filled with charred body parts and tries to clamp down on the slow burning of anger in the pit of his stomach at the thought of a terrorist attack in the middle of his city.
They get into a fight over that just a few hours later, when she berates him for "making it personal", and it pretty much sets the tone for how this case is going to be. It's both infuriating and fascinating to work with her – her total lack of tact or consideration in the interrogation room makes him cringe, yet she's the one to build a rapport with the suspect's wife, and he gets a lot of petty amusement out of the way she's freezing out Homeland Security. Agent Gibson is a good guy, but it's the principle of the thing, and Booth has a hard time keeping his face straight when Gibson complains to him that the "mad scientist chick" has refused to cooperate with anyone but her FBI partner.
In the evening, he takes Parker home from daycare but puts the babysitter on alert because SAC Santana has made it clear that he expects Booth to come back in at any given time during this case. It's a nightmare of parental logistics, but this is one case he's not going to hand over, and for once it has nothing to do with his career. He wonders how Bones handles things with her baby girl during times like this.
Santana doesn't disappoint, and Booth is just getting ready to leave when the doorbell rings. It's not the babysitter he's waiting for, though – for some reason, Bones decided that she had to deliver her findings to him in person. She starts listing facts, but stops abruptly when Parker comes running into the room yelling "Daddy, look!" and waving a newly finished crayon drawing at him. The awkward silence is filled with Parker's excited chatter; he doesn't even seem to notice her, and only Booth's admonition to say hello to their visitor makes the boy focus on her long enough rattle off a quick greeting.
She still seems taken aback, and Booth almost feels guilty for keeping the fact that he has a kid from her, but that feeling fades quickly when he reminds himself of her little secret that he stumbled across just the other night. Then the sitter arrives, and they're free to leave; Booth hugs Parker good-bye and ushers Bones out the door before she can get another word in.
He can tell she's curious, but he keeps his mouth shut on the way to the Hoover; he'll be damned if he gives her anything about his private life considering how she reacted to his perfectly justified question about her daughter's father. She can't keep quiet for long, of course, and starts going anthropological on him, but he'll have none of it. He's well and truly on edge now, and he finally gets her to shut up about her "solitary alpha male" crap by pointing out that he wouldn't have pictured her with a child either.
She's like a dog with a bone, though; as they proceed with the investigation of what has now turned into a murder case, she keeps bringing up Parker at every opportunity. She doesn't even stop when they run into Angela at Wong Fu's (those squints are like ants – once you have one in your place, the whole swarm follows), and when Bones walks out on him in a huff, he's left in the clutches of a crazy artist with zero sense of personal boundaries who immediately starts grilling him about his son's mother.
He wonders if Angela has any idea who the father of Bones' baby is, but he knows better than to ask her.
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She really wishes Angela would stop trying to play matchmaker. She knows that her friend means well, but Angela has all those outlandish notions of love and romance and what she calls "magical moments", and Brennan can't get her to accept that she doesn't believe in any of those. It's the reason she never told Angela that she had intercourse with Booth, and she's determined to keep it that way – she was very glad to discover that Booth shares her views on casual sex without emotional entanglements, and she doesn't want Angela to interfere with what she considers a very satisfactory arrangement. She and Booth both have very demanding careers and small children to take care of, so it makes sense to turn to each other when there are biological needs to be met.
She still can't quite wrap her mind around the idea of Booth as a father.
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They end up at Wong Fu's again when it's all over. It's late, and he really needs to pick up Parker from daycare, but he hates the idea returning to his child with fresh blood on his hands. Bones reminds him of the lives he saved, and even though it doesn't ease the familiar churning of guilt in his stomach, he's pleasantly surprised that she's trying to make him feel better.
He knows that there are things they should discuss, but after today he just doesn't have the energy. What he really wants right now is another drink, but Bones places her hand on his arm and tells him to go home to his son, and he's reminded that she, too, has a child to go home to; that they both have lives which don't intersect when there's no gruesome murder involved.
He has no idea if that's ever going to change, or if he even wants it to change, or if they'll go back to hating each other in a week, but right now they're okay, and he figures it's enough.