I blame Camille Saint-Saens 'Danse Macabre' for this one.
Also - John/Atlantis
Ever since that small crisis involving Rodney, a half charged-ZPM, a naquadah generator, the shields, and desperately trying to get the Atlantis to do what he needed, while dealing with the mass of information rushing in as he sat in the chair, John has always said Atlantis, baby, when he's talking to the city. Not out loud – he has no desire for anyone to start digging around in his head again, but when he's alone in the city, or really needs something to be done, and sweet talks her into it.
Sometimes he even imagines she calls him John-darling.
He knows who each life sign refers to on the life sign detector, and which ones are the Athosians, and which ones just don't belong. He knows Atlantis thinks of everyone in some particular way, just as he's the pilot/John/darling. Regardless of how many other people there are that she loves, John is always darling. Beloved.
Rodney is the – and there is a word/feeling that means something like chief scientist/investigator/experimenter/brilliant. Zelenka is the engineer/practical/calm. Beckett is the healer/researcher. Elizabeth is something that means leader and civilian and diplomat with flavours to each of the words that doesn't quite come across in English when John thinks about it, which he doesn't often. Teyla is alien/alone/dancer/leader/serene, and Ronon is the hunter that could be more, but is not.
This awareness isn't something he thinks about. It's just there, just as Atlantis is a constant thrum in the back of his mind, something that is there, and welcomed, but as little thought about as a favourite pair of socks. He feels at home here, as he hasn't done anywhere else, not even in the cockpit of a F-16. The puddlejumper is already more familiar and comfortable than any of the planes he flew back on Earth. And it doesn't matter where he goes in the city or the jumper, he is always home.
He goes back to the chair sometimes, when the scientists become involved in testing other things, and runs his hands over the armrests and feels Atlantis thrum slightly under his fingertips and welcome him. He doesn't sit in the chair, though. The seduction of the merger is too appealing, and he knows if he sits there, he's not going to get out until someone makes him.
And this is okay for a while.
He doesn't drift, quite. It's crisis up on crisis, week by week, it feels like, and it's too grounded in the present for drifting. He depends upon Rodney for the answers, and Atlantis learns to listen and anticipate what Rodney wants, even though she doesn't talk to him. She reserves that for John alone, and he's selfishly glad of it. Sometimes, the weekly crisis can be solved by military presence or action, and that doesn't make him feel any better. The two people he is closest to in the place is the city herself and an obnoxious scientist.
He falls into a relationship with Rodney almost by accident, brought out of events they don't care to question too closely, and a shared desire for non-violent physical contact. The events that lead up to it involved aphrodisiacs, a locked room, alcohol, and aliens. The events aren't too clear in his mind, but the sex is, and after they were both cleared by Beckett, and given medical leave for the rest of the day and the night following (barring any unforseen crises, of course), Rodney left in a hurry, silent, blushing and embarrassed. John knew he was blushing, but was more embarrassed at the public nature of their predicament.
So after Atlantis tells him that everyone who could be expected to be in their quarters were actually in their quarters, or at least, somewhere other than the living area, John goes to Rodney's door, thinking about that skin on skin contact, something he has missed since they came here, and goes in, seeking only basic contact, but gaining so much more.
Touch, for sure, what he wants, and more. Conversation, both serious and joking, public and private. John still reserves the right to dress Rodney down when he acted foolishly on missions, and Rodney never gives up insulting whoever he pleases, and calling John three kinds of idiot for doing his job.
Atlantis adds another term to Rodney's name.
John tells Rodney about his connection with Atlantis, and he tries to convince the city to respond to Rodney as she does to John, but the project has been of a limited success so far. She'll identify who is who on the life signs detector for him, but everything else is relatively subtle, and John only catches it half the time anyway. He doesn't know if she talks to Beckett, and he doesn't ask. Rodney teases John about having an affair with an inanimate object, and John doesn't say much, because after all it's partially true. And then Rodney says that he'd rather share John than not have him at all, and at least it's Atlantis.
Eventually, they decide that it would be easier to share quarters, rather than constantly having to go back and forth between the two for things left behind. They find somewhere entirely new, and settle in, between crises. Elizabeth throws them a house-warming party, and John realises with a feeling of glee that he and Rodney were openly and comfortably settled as a couple now, and that no one was going to say anything about it.
And the years pass.
The years are measured in Wraith attacks, and how many of the original contingent died, in crises, and in how many newcomers arrive. In the Pegasus galaxy, John loses track of how the years are passing on Earth, and only notices new technology when it arrived, and makes their lives easier. The Pegasus Galaxy and Atlantis are home now, and he feels more inclined to go somewhere on the mainland or in their galaxy when he takes leave than go back to Earth.
He goes back to Earth with Rodney, though. Meets Rodney's sister and parents, and introduces Rodney to his own parents. The meeting is less than successful,but they visit all the relatives every time they go back to Earth, once a year or so. And after the Stargate Program is revealed to the public, and the Atlantis Project is acknowledged, visits to Earth are filled with press conferences and publicity shots, until neither of them can deal with the sheer stupidity of their fellow man anymore, and escape to ride ferris wheels and eat take away.
Earth food doesn't taste quite right now.
The best part about going back to Earth is standing in a small courthouse in Canada with Rodney, and vowing to spend the rest of his life with him, something John had been planning to do anyway, and this only formalised the deal. He wears a ring now, and the newcomers to Atlantis always sigh when they realise he's taken. What they don't understand is that John would be taken anyway, caught up in Atlantis as he is.
They're showing a group of newcomers around a bit of the mainland with some of the Athosians. Rodney is in the lead, with a science-groupie beside him, and another behind him, gesturing expansively. Ronon has their six, and John is trailing somewhere in the middle, trying to make the shyer ones feel more at ease. And then Rodney suddenly clutches his chest and falls over. He's dead before he hits the ground, and John feels him die in his head. The connection that Atlantis has with his husband suddenly winks out.
He kneels by Rodney, trying frantic CPR and mouth to mouth, with some of the groupies, while others summon an emergency medical team and a jumper. But they don't carry a defibrillator pack on them on these training walks, and by the time the jumper gets there, it's far too late.
Beckett tries for over an hour back in Atlantis, and John can feel the city trying to help him, but the connection simply isn't there anymore, and all he can do is sit and wait. Elizabeth waits with him, and Teyla, Ronon, Radek and the groupies. As time passes, more people drift in, waiting for news.
When Carson comes out, the connection still isn't re-established, and he doesn't even need to look at his face or hear anything to know that Rodney is dead, and suddenly his life is empty. They don't leave him alone. Even when he retires to their bedroom, there is still someone in the lounge, in the hallway, on the balcony. No one is quite sure of what he will do now, or what to do next, and John knows that he'd better not appear suicidal, or they'll send him back to Earth, for his own safety, and he won't survive a double-widowing.
Atlantis grieves with him, just as she has for every person he has lost, and that helps, as much as anything does. They have a wake, and a funeral. Rodney's family are shipped in from Earth, and there are tears and condolences. But John doesn't know what to say to them. How does he explain to people that he has this connection to the city, and through her, he can find everyone in the city? How does he tell them that he devoted a part of his brain to constantly tracking where Rodney is – was – and now there is a space where there shouldn't be a space, so he is constantly searching for that particular life sign, and it isn't there. In the end, it's too hard to say, so he says nothing at all, and just nods and accepts what people say.
Instead, he draws on his connection to Atlantis and the list of every living person in the city makes a semi-comforting murmur in the back of his head when he's trying to sleep, and is a focus for when he thinks he's going to cry.
John's been to a lot of funerals in his time in the Air Force. He never expected to be attending the funeral of his husband in the Pegasus Galaxy, but life throws some strange curve-balls at times, and he wouldn't have missed out on this for the world. They send the coffin into the sun, launching it out of Puddlejumper 1 from the appropriate vector, and knowing that since there is no friction in space, momentum will just keep it going until it burns up. John thinks that if they couldn't inter him below Atlantis, and the city assures him that there is no room, that this is the next best thing.
Elizabeth relaxes a bit after the funeral, evidently thinking that if John was planning anything suicidal, he would have done so by now. So it isn't hard to sneak off, and with Atlantis' help, avoid seeing anyone, until he reaches the control chair.
The doors are locked, of course. They don't want anyone getting in here by accident, after all. But John isn't the senior military commander of the city for nothing, and even if he wasn't the military commander, he is still the darling of the city, and she would let him in.
He hasn't been here alone for years.
The last time he was here, it was another emergency, and Rodney had dragged him in here, told him to do his thing, sweet-talk the city, whatever, and had promised to guard him, and make sure he came out safely. John hadn't wanted to leave the chair, but Rodney had sent all the guards away, and used the one thing the chair didn't provide to lure him out – physical sensation.
But Rodney isn't here now. Rodney won't ever be here again.
John sits in the chair, and feels the full attention of the city.
"Atlantis, baby," he says. "I'm all yours."
Summary: John loves Rodney. John loves Atlantis. There is no choice.