Obviously, I don't own the show or characters, just this story.
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At first it's just arguments. The differences between you are the only apparent thing. He relies on his gut, you on science. How the two of you actually solve cases is, at most times, beyond you. His chauvinistic attitude and distaste for anything "squinty" infuriates you. You resist his charms and that infuriates him.
Then there are the special cases. The cases that show he's more than just an alpha male. The cases that show that he cares for the victims, truly wants justice for each life lost. Soon there are nights with Chinese food and movies, jokes and smirks. And you start to think that maybe you can overlook the unscientific approach he takes, and maybe consider him a friend.
Soon there are tears. Parents lost and found, moments of weakness, self-doubt, and indecision. You meet Sully and your life feels infinitely better, until another person you love leaves. Through it all, there he was. Drying your tears, promising 'someday'. There's Jasper and eventually a "Brainy Smurf', reminding you that he does listen, and you can't help but want to feel that maybe not everyone will leave.
When he dies then comes back to life, you feel betrayed but can't help but look to him for comfort when everything falls apart. As you become closer still, you find yourself burying forbidden feelings deeper than ever. There's the line and don't want to deal with the chance for loss yet again. He's your best friend and he'd opened you up but that final stone can't be removed. After the incident with the brain tumor, he scares you, but comes back again, helping you breathe once more. In the following months, you begin to feel the shift between you. He finally erupts one day, telling you those three words you are most afraid of. You run.
Things go back to some semblance of normal after that. He tells you to forget it, don't worry about him, but you can't help it. You both go back to working cases, and everything feels okay—until the accident. Even though it's only his shoulder, you worry incessantly until you can see him. He's on pain killers and going on about missing out on something and you apologize, but for what you aren't quite sure. He focuses his russet eyes on you and you are overwhelmed by the emotions swirling from the depths of your heart. You finally say those three words back and he freezes. Your eyes are teary with emotion and you wait for him to hug you, smile, anything but the shocked look overtaking his handsome features. Your own smile falters as he tells you that he can't. He's been dating Agent Perotta and he just, can't. You stutter out an apology, and turn around, not wanting him to see your tears. He stops you as you reach the door, saying he's so sorry, and you can only nod in silent, sad agreement.
You remain his partner, though you start reconstructing the walls he so carefully tore down. He has Perotta, you have skeletons. Soon there is a wedding, a honeymoon (though neither is yours) and you tell him (and everyone else you have to) that you are 'so happy for him', though you hate the fact that you aren't. Life goes on and he doesn't, can't, spend nights after cases with take-out and a movie. He tells you that he's still your friend (you both smile at the lie), that he'll always listen (except when she's waiting for him), that he'll be there for you (except when she needs him) and you go along with each lie, not wanting to break the façade.
Finally after one case, he asks you for a drink. You go to the bar, sitting next to each other in silence. You can tell something has changed, but don't mention it. After a while you both leave for home and you aren't sure who is more discouraged about the prospect. Eventually these nights become more frequent and he finally tells you. There are lawyers and divorces and irreconcilable differences. You find out from Angela that part of it is that he didn't want to, wouldn't, leave D.C for her, and it opens up a window. You aren't sure who hates that more.
Months later, after closing another case, you stay at the lab. There hasn't been anyone to make sure you go home at a decent hour in a long time. You drive past the Hoover Building on your way home and unconsciously look up at his office window. It's ablaze with light, even at 12:25, and you feel yourself pulling the car into park by the curb. You walk up to his office (thankfully the security guard you knew was there), and lean on the doorframe as you watch him stare off into space. When he finally looks up, you see the shimmer in his eyes and can only apologize softly. He nods and bows his head, hiding the pain dripping slowly down his cheeks. You cross the room quickly and put your hand on his shoulder, not knowing what else to do. When he finally puts his hand on yours in a silent acquiescence, you feel that final shift and know it will all be right again soon.