Sheppard wakes up in his room on Atlantis with no memory of who he is or where he is. He goes out of his room and discovers that he's the only person on Atlantis. Everything but the gate works. He can't find any evidence of something going wrong - for him to be alone or why the gate isn't working. Exploring the city, he finds that the computer laptops work and starts going through them, learning about the city and the people there. Eventually he discovers Rodney's lab and begins going through the work logs and finds out that the science department had been working on shifting things out of phase using some Ancient do-hickey and that he was helping with the experiment.
It'd be a cool story just because we'd get to see just how smart Sheppard is because he'd have to complete the experiment or fix it and come back from being out of phase (of course, he'd probably assume at first that the rest of the expedition are the ones out of phase until the clue bus hits him that if this was true - the gate would still dial out), also the story would work well with getting into learning about himself and his friends because he'd have to learn about them from reading their logs, journals, video files, and mission reports. Though I don't think that Ronon would be too much with the computer logs/journal thing but it'd be cool for Sheppard to find written journals of Ronon's.
(though in my head I could see Ronon's written journals being letters to Melena, and could point to him sorta asking for her blessing, in a way, for Ronon to feel something more for Sheppard than just as a friend. that's just cuz they're my OTP and I think it'd be an awesome way for Ronon deal with guilt over falling for someone else and also for Sheppard to understand more about Ronon. This wouldn't be essential for the main plot of the story though.)
After he gets 'back', (his memories completely restored) Sheppard finds out that Rodney and the others thought they'd pretty much vaporized him but then he explains what happened and that he fixed things himself and how he did it and the others are surprised and impressed that he'd done it all on his own. Though it might also be a cool way to employ the Sentient!Atlantis idea in a way. Even if she can't outright help with fixing things, she can point Sheppard to things to help him learn about himself and the others.
Story could be totally gen but it'd also be a great way to do a cool amnesia fic with some Sheppard/Ronon since I haven't found any of those yet. But if you like the idea - have at it!
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