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I recommend reading any and all of Blackchap's stories, but this is one of my favorites. Most of Blackchap's stories are mature/explicit.
Bound Together
http://archiveofourown.org/works/250919
Author's summary: John's life changes completely after he arrives in Atlantis: his higher-ups think he's been compromised, and he doesn't want to command, but has no choice. The entire expedition is in peril as he fights to keep both the Wraith at bay and prevent a city-wide mutiny from destroying everything he's sworn to protect.
Blackchaps Blog (more stories than on AO3):
http://blackchaps.wordpress.com/
No longer working.
Blackchaps SGA stories at AO3:
http://archiveofourown.org/users/blackchaps/pseuds/blackchaps/works?fandom_id=70
Bound Together
http://archiveofourown.org/works/250919
Author's summary: John's life changes completely after he arrives in Atlantis: his higher-ups think he's been compromised, and he doesn't want to command, but has no choice. The entire expedition is in peril as he fights to keep both the Wraith at bay and prevent a city-wide mutiny from destroying everything he's sworn to protect.
http://blackchaps.wordpress.com/
No longer working.
Blackchaps SGA stories at AO3:
http://archiveofourown.org/users/blackchaps/pseuds/blackchaps/works?fandom_id=70
