A/N: I had no idea there was more to this story, and I have no idea how much more there may be. I'm just as surprised as you.
John didn't look up, didn't say anything, just shifted position to hold Rodney tighter. Carson exchanged a look with him and radioed the infirmary, canceling the EMT's. Another look, between the physician and Elizabeth, carried so much unspoken dialogue that Caldwell felt, for a moment, that he'd gone deaf.
"I'm very sorry for your loss, Doctor McKay," he said stiffly. The scientist didn't seem to hear him, still weeping raggedly onto Sheppard's shoulder. As he watched, the soldier began to rub McKay's back in long strokes, smoothing out the wrinkled shirt.
Caldwell cleared his throat abruptly. "Lieutenant Colonel, I'm sure Doctor Beckett can handle this. I have some concerns I'd like to discuss with you before the Daedalus sets off for Earth again."
He wasn't prepared for Beckett's sudden glare of undisguised outrage, for Sheppard to ignore him completely, or for Elizabeth's hand on his arm, surprisingly firm, pulling him away. His astonishment lasted long enough for her to drag him out of the conference room, closing the doors behind them.
"Let's leave them alone for a bit, Colonel." Her voice was hard and cold. She stalked toward her office, glancing back only once to make sure he was following.
The moment the door of her office closed, she turned on him. "I'm sorry if Doctor McKay's reaction to the news of his sister's death or the comfort offered by his friends makes you uncomfortable, Colonel, but I will not permit you to disrupt his grief with minor administrative issues. Rodney now has no family left on Earth. He's going to need the support of his family here on Atlantis, all the support we can give him."
"Look, Doctor Weir," Caldwell jumped in, "I support 'Don't ask, don't tell'. What Sheppard and McKay do in private, off duty, is their business and not something I can control, whether I think it's detrimental to their team or not. But that kind of public display of affection is completely inappropriate, and it's going to get them in trouble. I can't pretend not to have seen it. I'll let it go this time, out of deference to Doctor McKay's loss, but it can't happen again."
Elizabeth's eyes had gone wide. "You think – that John and Rodney…" She walked around the desk and sat down heavily, leaning her elbows on the desktop and putting her head in her hands.
"Colonel…do you have much experience with the Gate teams at the SGC? I know your qualifications to command the Daedalus, your experiences in various hot spots on Earth. I know you've been through Earth's Stargate on missions. But have you seen the kind of friendship, the deep rapport that Gate teams develop? SG-1's exploits are legendary among those who have the security clearance to read their mission reports. They've defied death again and again, triumphed over impossible odds, experienced things most people can't even imagine. The affection between them is unmistakable, and to the best of my knowledge, none of them have had physical relations with each other."
She raised her head and gazed straight at him, her sharp eyes searching his.
"Here on Atlantis, we were cut off from Earth for the better part of a year. Just a few hundred people, living in each others pockets, under constant threat from an adversary that could drain the very life from us with a touch. We've had to rely on each other, without any backup, no supplies or equipment except what we brought with us, what we could trade for, what we found and could make work in Atlantis, in the knowledge that every day could be our last.
"We can't go home at the end of the day, Colonel. Leave time is spent in the same place we work, with the same people we work with. Friendships here reach the same intensity as romantic relationships, without any sexual aspect necessary. If you find yourself that uncomfortable with seeing a man offering comfort to a grieving friend, if you're that ready to jump to unwarranted conclusions…you might want to consider resigning command of the Daedalus. Because there's nothing physical between Rodney and myself, either, and I would prefer to be in there with him, holding him, rather than disabusing you of your unfounded suspicions."
"But you're – "
"A woman? I'm also in command of Atlantis, Colonel. It would be inappropriate for me to get involved with the head of my science department. Nevertheless, Rodney is my friend, and as such, no one on Atlantis – none of the original personnel – would consider it inappropriate or suspicious if I were to hold Rodney the same way John is holding him now. And none of them, seeing John comforting Rodney, would entertain the notions you have."