1 - Stories where someone try to remove John from Atlantis and all the expedition band together to show their support and avoid this. Or maybe is John who is thinking in leaving because he's mentally unwell and thinks he's useless/screw-up and everyone show him this isn't true.
2 - Some higher-up (the IOA and/or the Pentagon/Air Force) wants to remove John because they want someone more by the book and controllable in charge and manage to suceed (maybe trying to kill him and leaving him seriously injured, causing a medical discharge or setup him with false accusations for a court martial and dishonorable discharge). Months or even a few years later they discover they commited a serious mistake because none of his sucessors is doing well (dying or quitting) or Atlantis herself is causing problems (AI missing his presence). I want someone from SGC and/or Atlantis going after him but he refuses to go back because he's still angry and bitter, especially if no one from Atlantis tried to help him (ex: defending him when arrested) or even visit him before. A change of mind only if they undo the damage (at least punishing the ones who destroyed his career, a formal apology and a good explanation if his 'friends' from Atlantis abandoned him). If he really refuses, will like to see the reaction at the SGC/Atlantis, especially if they are feeling guilty for leaving him behind for starters. One story I found which is almost what I'm looking is Atlantis Reborn
, but is WIP and John isn't really alone here.
3 - Some DADT-focused stories where John isn't gay or bi but helps to defend members from expedition who are
4 - Stories where Rodney is interested in John and thinks the opposite is true because of their friendship but is unable to say something. Them he uses a situation where John is defenseless (drugged, brainwashed, mind control or something similar) to get him to bed because he thinks he will like, but he's mistaken because John isn't gay/bi or maybe was abused in his past, then when he recovers and discovers what happened he's very angry with Rodney for abusing his trust. I already read similar stories in the past but normally they end with John discovering/admiting he likes men and going to bed again with Rodney like nothing bad happened. I want a more realistic reaction because gay or nor this is rape, not interested in John being homophobe, much less going to bed willing with Rodney again.