Among The Danger And The Physics.
The fact that he was attracted to her at all should've told him something, but amidst all the danger and the astrophysics, he really hadn't had much time to contemplate it. His crushes were all blonde, his last three girlfriends had been blondes but then, they never lasted. A month, maybe two, long enough to say that he wasn't celibate, short enough to tell himself that he didn't care.
He didn't let himself think about whether he really did care or not.
Elizabeth was brunette and he defiantly cared about her. Not that he had much time to think about it what with the danger and the quantum mechanics, but sometimes alone and stuck (not stuck - pausing) on an equation or trying to sleep in his quarters, he thought there might just be something about Elizabeth Weir that meant he could stand to be around her for longer than a month (or two). His blondes always came up short to his expectations. Not that he ever did the dumping but he told himself that he would've. Given an extra week.
Rodney McKay needed perfection without exception. Which was why he always got along better with numbers.
He got on really well with Elizabeth.
He hadn't noticed at first, what with the danger and advanced mathematics and all, but she had a patient smile, that she used on him a lot. It was a little different to the one she used on John, there was always amusement or frustration in her eyes when she smiled patiently at Sheppard like that, but when she smiled patiently at him there was something in her eyes that he couldn't define with equations.
Once Atlantis became home and the desperate need to look at every piece of technology had faded a little, he began to notice little things about her. His attention was diverted away from danger and cosmology (he had to have a hobby) by Elizabeth Weir. Which was unusual because he didn't put people before physics.
When she bent over he was caught off guard and found himself staring. He didn't have time to stare at anything usually. When she put her hands on her hips, her breasts were thrust out and he really liked that but couldn't stare. When she was amused her mouth quirked and it was the cutest thing.
He didn't find many things cute, there was nothing cute about calculus.
He avoided the L word but he definitely lusted after her because appeared in more fantasies than Sam Carter did unless they were both together. Most nights when he felt out of place surrounded by danger and biology (he'd never say it out right but it wasn't his strong point), he thought about Elizabeth Weir and how she always made him feel welcome.
The fact that he was attracted to her didn't tell him anything, but amidst the danger and the politics and the kissing, the fact that she was attracted to him told him everything he needed to know.