Disclaimer: Not Mine. No Money. Having Fun. Etc.

AN: So, I keep trying to figure this out in my head, so I decided I might as well get it down on paper…or computer. Whatever. I love the way Domenika Marzione explains Atlantis' sentient capacity and John's connection to the city. I'm taking the basis of that idea, that Atlantis communicates in something resembling worded images and likes to show John all her secrets, and trying to understand John's view of the whole thing. But I give credit where credit is due, because she does it so much better than I do.

Atlantis has a different relationship with anyone with the gene, either naturally or artificially. Rodney never talks about his; because that would mean admitting that the city is, at least, partly sentient and he can't quite wrap his physics specific brain around that concept. He's never been into the idea of AI before and he figures it's a little late to start now.

Carson's been scared of Atlantis since he set foot on her. Probably longer, in reality, John thinks, after the whole drone accident on Antarctica. He hesitates before he touches anything Ancient tech he's never touched before, and only uses the medical tech on a regular basis because it makes his life easier. The few times he's been called upon to sit in the chair have made John realize that things are not going to change. He think that maybe that's okay, because Carson is damn good at what he does, and John's damn good at what he does and things have worked out just fine that way for three years, so why change a good thing? Carson has only once mentioned that he can hear Atlantis in his head. It was to John, and the expression on his face was part 'I know I'm crazy for saying this but I feel compelled to anyways' and part 'please, please, please tell me I'm not crazy'. John had told him he was only crazy if John was crazy and when that didn't seem to alleviate Carson's fears he'd resorted to telling Carson just how much Atlantis actually said to him. The look he'd gotten was 'well, you might be crazy' and then there had been scans and tests and John had wisely never brought the topic up again in Carson's hearing.

John hardly ever mentions his relationship either, but that comes more from that fact that he knows Rodney will just get all jealous and less because he's freaked out by the whole idea of having a city in his head. He tells himself he's not. But he's just a little worried, somewhere deep down inside, that if he actually comes out and says it he'll be shipped off to Earth for mental instability, or at best sent down to Heightmeyer's office, and he'd rather encounter the Wraith again then listen to her talk for an hour. But even if he won't admit it out loud to anyone who doesn't understand, it doesn't stop him from admitting it to himself. Every few days he reroutes the path of his morning jog so that he ends up running passed the access door to the east pier. He stops, walks outside, and stares at the ocean for exactly ten minutes while he lets Atlantis flow through his mind and show him all the things he never lets her show him the rest of the time. He then resumes his jog as if nothing has happened, which he can, because Atlantis loves him like the long-lost son that's finally returned home and he knows his ten minute pause has gone unnoticed by the tech guy who watches the internal sensors.

Only very rarely does he abuse his connection with the city. But there are times – usually after they've come back from a mission that's ended in disaster and he's not the one in the infirmary – that he finds the nearest place where he knows he won't be disturbed and lets Atlantis hide him. He knows, because she's mentioned it more than once, that Elizabeth is both annoyed and worried when he drops off the sensors. But she never does more than mention it because they both know he's safer in Atlantis than anywhere (and with anyone) else and that he needs the alone time as much as she does. He just goes about it a different way.

He's caught Lorne at it too, more than once. He is, in fact, the only one who has caught anyone else at it, because unlike everyone else, there is nothing the city hides from John. He can go wherever he pleases and ask whatever questions he likes and she will always answer. And she may like his XO enough to hide him every now and then, but she loves John enough to let him know where Lorne is when he needs to know.

Some small part of him is secretly amused by this. And proud, because he's never been the beloved of anyone or anything before. He's also a little freaked out by that thought. Atlantis is part guardian, part mother, part older sister, part therapist and there are days he wonders if he even needs anyone else. Because Atlantis never snaps back at him in anger, never judges his decisions, always forgives him; he's never had unconditional love before and he finds it both ironic and typical that the first time is an AI city on the other side of the universe. He's also kind of attached to it. And he supposes that that's a sign of mental instability more than anything else, because he actually has feelings for the city. He loves her and wants to protect her and really, really doesn't want to share her. He can't explain where that feeling comes from, because he knows he does, in fact, share her with others, but he's never aware of it as something conscious and he supposes that that makes all the difference.

Rodney has once, in that amazingly sarcastic voice of his, referred to John's relationship with Atlantis as akin to a five-year-old's obsession with legos. John's a little put out by the comment, but mostly because he finds it highly unfair that unlike legos he can't take Atlantis apart and rearrange her pieces. Because that would just be cool. But he also realizes that Rodney is, at least at face value, right in his analogy. John went through the whole obsessed with legos thing, though he was four at the time, and he remembers that he played with them constantly for more than a month before they were taken away and he was given something else to distract him. He remembers crying, the only time he can remember crying during childhood, and that he moped around for more than a month afterwards, surviving by playing with the legos at day care, which weren't nearly as fun or as plentiful.

Sometimes Atlantis does feel like that, because he knows that if she is taken away he will react much the same way he did when he was four, except perhaps with less crying. But he also knows, inexplicable, that she will in fact be taken away, that he will never voluntarily leave her. Because she's the first thing to love him without reservation his whole life and he's not about to give that up. She's been more calming, more patient, and kinder than anyone he's ever met.

He steals outside to the highest balcony next to the Control Tower in the late hours when most of the city is sleeping, except for the night staff. Atlantis is dim, but not dark, not with a fully charged ZPM at their disposal. He watches the ocean from high above, stares at the moonlight reflecting on the waves, and lets Atlantis hum through his mind. She's excited today, he can feel it. He lets her in enough to feel her emotions but not enough for her to actually talk to him. He's too tired and wants to get to bed and doesn't want to be running around the city at all hours looking for the next thing she wants him to find. That's what the mornings are for. A scout team has uncovered another lab on one of the lower levels, full of information only scientists will find interesting, but Atlantis is happy about it. Tonight she's dancing colours in his head, so that when he closes his eyes it's never dark, but a rainbow of colour and he can't hear the crash of the ocean over the pleasant hum of the AI. It's just like every other night.

He knows that if she's ever taken away from him he'll miss the nights most of all. When there's nothing for company but love and colour and a sense of belonging he's never felt before.

He thinks a part of him loves her back more than he's ever loved anything.