Brenda doesn't know when she began to feel this way. She does know that is wrong. She watches him from her office sometimes, hoping not to be caught. If he happens to glance up, she quickly manages to be looking elsewhere. One of these days, she's going to get caught, however.
Her husband suspects something is amiss. Things haven't been quite the same between them for quite sometime now. Oh, their lovelife is active enough, but it's like her heart isn't in it anymore. It's no longer him she's thinking about, it's someone else. And she knows it's wrong. But she doesn't stop it.
One day, he has to drive her to the crime scene, Gabriel is doing something else, so she asks Flynn to take her. She thinks she's being surreptitious with the little glances she throws his way, hiding behind her glasses. But he knows. He's finally catching on. And he discovers he likes being the object of the Chief's affections. He also knows that if he were to flirt back, something might come of it. But he doesn't. He won't be responsible for the break up of a marriage. He'd been subjected to that with his last wife and he couldn't do it to anyone else. He doesn't have it in him.
However, he soon breaks his promise on flirting back. Whether it's the way she's talked to him(that southern drawl that has a hint of softness and persuasion in it), or the way she stands close to him at the crime scene, he breaks. He uses the excuse of helping her in order to touch her, to have any kind of contact with her. He can't help it.
Soon, he's looking at her in her office, hoping to not get caught by his co-workers. Every once in awhile, his eyes meet hers and they both smile, before quickly looking away. He honestly doesn't know how long he can keep this up. His feelings are growing stronger, but she's married. And even though she flirts, he knows she won't leave him.
Then, one day, she stops. No more surreptitious looks, no eye contact, no flirting. He doesn't know what he did wrong, but he misses it more than he can say. In fact, if she does happen to look at him, her face is filled with guilt. When her husband starts coming to the office regularly, he can tell there are problems between them just by the way they interact. He seems to be checking up on her, and Flynn clues in. The husband has figured out that his wife doesn't feel the same way as him anymore. He's becoming more possessive, trying to figure out who his wife is thinking of. When Chief Pope comes in, the husband wrongly thinks it's him and treats him badly. When Chief Pope leaves, Brenda closes the blinds, but the team still hears the argument that occurs within the walls. A few minutes later, the husband storms out, pissed by the argument. It's the last the team sees of him.
Months later, one day, Flynn sees the Chief looking at him again, a smile crossing her face. He smiles back at her. Their flirtation starts again. She seems happier, more willing to talk, more willing to be around him. And he knows things have really changed when they're walking the three blocks together to the parking lot after work. They're strolling along, talking about much of nothing. It's evening, the shadows are thickening and it's a warm summers evening. She suddenly grabs his tie, pulling him into an alley. They stare at each other for a second, before she's pressing her lips to his. He can't help but respond, he's been waiting to do this for so long.
When they break apart, he looks at her questioning, before grabbing her hand, looking for her rings. They're gone. He looks back at her, she smiles. He suddenly understands why she's been flirting again and FBI guy has disappeared. He pulls her close to him, kissing her intensely. He doesn't know where this will go, if it will go anywhere, but he's happy. She's happy. And for now, that's all that really matters to them.