They're so different.
That's what he thinks when he first meets her, poring over some old bones (as if that's any way to catch a murderer) and treating him as if he were an ignorant child for wanting to use his instincts, his "gut". (Of course, she turns out to be right about those "old bones," but that's a whole 'nother story.) How can he get along with someone who openly mocks his beliefs, his religion, his sense of what is right in the world? He forces down his attraction (it's just… frustration, that's all).
They end their case and he is relieved to be away from her overwhelming intelligence and arrogance. Thank God he's rid of her. He'll never have to work with her again.
They're so different.
That's what she thinks when she first meets him, barging into her lab and telling her that her way is wrong, that some "old bones" won't prove anything, that she should let him do what he does best. He simply won't listen to reason, which is evident in the way he runs his life. How could any relatively intelligent, reasonable person be so attached to "gut feelings" (after all, a gut can't feel), and... religion, of all things? (Everyone knows that some omnipotent being couldn't possibly have created the world in seven days. Evolution, after all, takes millions of years.)
Obviously, she proves him wrong (of course she was right about those bones), and is relieved to learn that soon she'll be away from him, and thus her unreasonable and disconcerting attraction towards him. (She flinches away from that which she does not understand).
They are so similar.
That's what they've learned from their five years of working together, the five years in which they have become such close friends. (Could they be more?) Sure, he is religious, still believing in reactions and "gut feelings", and she is still the rational empiricist, asking that everyone abstain from jumping to conclusions. (Except him, she lets him jump… but why?) However, each has learned so much from the other, both in terms of crime fighting and the far more personal, indescribable relationship that they share. He's learned about logic, and reason, and science-(he even understands some of what those squints are yammering about, a personal achievement). She's learned so, so much about feelings, about opening up to others, about love. (She even thinks that maybe, just maybe, he is right about love. Maybe the heart feels first and the brain's reaction follows). And every time they realize that they share still more, their hearts leap, although they won't admit it to anyone, and certainly not to each other or even themselves.
Although one believes in God, and the other believes strictly in that which is based on fact, they once again discover a similarity while conversing over their customary coffee. Their faith has been shaken, and each must find a way to rediscover it, whether by praying or by adding two and two and getting four. Eventually, both will regain their lost faith, (interestingly, what has never wavered is their faith in each other) and will continue down their shared path… to what? Perhaps they won't admit it now, but they will eventually.
And perhaps they haven't allowed themselves to realize how their love (born of such close friendship and mutual respect) has grown, but they will.
Eventually.