Spoilers for "Critical Mass"
Stargate: Atlantis belongs to someone else.
by Brat Farrar
John had wanted to say No, no—we are different, we are nothing like the Wraith, but he couldn’t find the words to explain, and Elizabeth wouldn’t be willing to listen, anyway. That was obvious in the set of her eyes and mouth, the tension in her shoulders. So he put on his I’m thinking about it face and left as soon as was polite. The excuse he gave was the need to find a camera before Radek undid the kids’ handiwork, but mostly John just wanted to escape Elizabeth and the evidence of another small failure on his part.
He could see now that he should have convinced her to let someone else head up the investigation, should have made her stop and look for evidence before moving on to interrogation, should have looked beyond the dislike everyone had for Kavanagh. But he hadn’t, and now she blamed herself for the outcome—never mind that they were still all alive and unharmed. Thank heaven for Cadman's stubbornness. They’d even saved Caldwell, although it had taken them a horrifyingly long time to figure that out.
The Wraith wouldn’t have given a second thought about Kavanagh, probably wouldn’t have bothered trying to save Atlantis. They would have simply cut and run, or else started sucking the info they needed directly out of peoples’ heads.
If John was like the Wraith, he wouldn’t be having nightmares of being trapped in his own body, of no one noticing that it was someone else looking out through his eyes—of the line blurring between 'John' and 'not-John' until there wasn't any left. He wouldn’t keep himself up at night wondering how long Caldwell had actually been someone else. He’d nearly hated the man, after the whole nearly-turning-into-a-bug fiasco (and he still had plenty of nightmares about that), but what if it hadn’t been Caldwell at all?
No one else seemed to care about it though, so he told himself to stop thinking about it and just keep doing his job.