It wasn't the sort of thing you noticed, at the beginning. It was really just a case of all the parts adding up to a bit more than their sum. It was like slowly raising the heat on a pot of lobsters. Nothing but gradual changes, all going unremarked upon until it was too late. Then came the inevitable conclusion: a Hot Fiery Death.
When they sit together in the mess, with Teyla and Ronon, there's was always a circus of motion before the eating begins. John would pass his jell-o cup to Rodney in exchange for the Chef's sad attempt at lemon squares. Whenever they had those salads with the weird Athosian nuts, Sheppard would quietly pick them off with his fork and dump them swiftly onto McKay's plate. It was a quiet ritual, the sort of thing that passes between friends who know each others tastes. Rodney never raised an eyebrow at their mealtime antics.
Everyone knows Rodney isn't so great with a gun. So, as a favor, (though McKay sure didn't see it that way) Sheppard decides to help him with some target practice. John claimed it was because all of the marines we too scared to teach McKay themselves, but Rodney knew there was some genuine friendship behind the action. Maybe that's why he shows up and puts forth some effort, going so far as to actually hit the paper targets occasionally. Rodney improves continually, and so he didn't comment on the fact that John stands a little too close, brushes up against him to provide unneeded adjustment to a stance that was fine to begin with. McKay writes it off as Sheppard being a perfectionist and doesn't say anything.
Sure, John was team leader. But did he really need to keep up with the goings on of Atlantis' resident genius so closely? Probably not, but Rodney doesn't complain when John stops by the labs before lunch to hear about the latest projects and to tease Kavanaugh a bit. Sheppard's always helpful and isn't in the way, so Rodney doesn't really mind that John leans in close behind him sometimes to point at equations on the laptop screen. It was only John, so what did a bit of personal space really matter?
McKay hadn't seen a single movie all month. He'd been swamped trying to fix the environmental controls (snow, novelty that is was, wasn't welcome in Atlantis), and hadn't managed to get his hands on anything from the last Daedalus run. So when John comes to him with the offer of a Star Wars marathon and real popcorn, he readily accepts, too excited to notice the Colonel's nervous smile.
John arrives at Rodney's door at around 2200, movies and popcorn in tow. Rodney greets him enthusiastically by snatched the DVDs, and they settle down next to each other on Rodney's bed. They take their usual position: laptop resting on Sheppard's thighs, the bag of popcorn in Rodney's lap. McKay's too busy enjoying The Force to notice when, during a grab for popcorn, John scoots towards him, their legs pressing together and shoulders brushing. Just as the popcorn runs out A New Hope's credits begin to roll. John had every intention of staying awake for all of Empire Strikes Back, but he finds himself drifting off, eyes like sandbags, and he can't quite resist the pull toward sleep. It's been one hell of a week, and really, what does it matter? He gives in to his subtle temptation, and leans into Rodney, resting his head against Rodney's shoulder.
Rodney looks up from the laptop screen and over towards Sheppard's head. His faces twists in thought, and after a few moments he lets out a soft "Huh" as the puzzle pieces fall into place. He gently clicks the laptop shut and places it onto the stand next to his bed. He yanks a blanket up from around his feet and drapes it around the two of them. He lays down on his bed, comfortable, and pulls John down with him. They lay there, quietly, and drift towards sleep.
All this time John's been quietly turning up the heat, gradually, trying to avoid a panicked reaction. Rodney's realization might make him a dead lobster, but this is one fiery demise he doesn't feel like avoiding.