Not quite what you're looking for, maybe, but there's a Keira Marcos fic -- where O'Neill and Jackson go to Atlantis and O'Neill is prepping John to be in charge... "Human Nature"... but you have to build an account on her site to get access. http://keiramarcos.com
Survival + Snippets (http://archiveofourown.org/series/302247) series by ZedElla (Leviarty) Written by the Victors (http://archiveofourown.org/works/15) by Speranza
In those ones John assumes the leadership more near the end of the story but some will have sequels: The Silent Language of Grief, Book One (http://archiveofourown.org/works/2858819) by water_4_willows Tilting of the Axis (http://archiveofourown.org/works/4550724) by Starkindler You know nothing (http://archiveofourown.org/works/1908267) by hellbells
"Written by the Victors" was already mentioned, so I have these to add:
Repercussions by crazy_obsessed (McShep) http://crazy-obsessed.livejournal.com/9248.html
Finding Home by Diamond-Raven (McShep, back in Atlantis later) http://sgabigbang.talkoncorners.net/?view=fic&id=37
The Sentinels of Atlantis verse by Keira Marcos (McShep) http://keiramarcos.com/fan-fiction/stargate-atlantis-fan-fiction/the-sentinels-of-atlantis-atlantissentinel/
Into the Whirlwind by slybrarian (Sheppard/Lorne) http://www.wraithbait.com/viewstory.php?sid=14053&index=1
And as a bonus: Evil Overlord Sheppard by GraceandFire https://archiveofourown.org/series/2541 AU: Sheppard is not in charge of Atlantis, but in charge of his own planet.
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Date: 2016-02-12 02:58 am (UTC)no subject
Date: 2016-02-12 06:17 pm (UTC)Written by the Victors (http://archiveofourown.org/works/15) by Speranza
In those ones John assumes the leadership more near the end of the story but some will have sequels:
The Silent Language of Grief, Book One (http://archiveofourown.org/works/2858819) by water_4_willows
Tilting of the Axis (http://archiveofourown.org/works/4550724) by Starkindler
You know nothing (http://archiveofourown.org/works/1908267) by hellbells
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Date: 2016-02-12 07:11 pm (UTC)DM
no subject
Date: 2016-02-12 07:12 pm (UTC)DM
no subject
Date: 2016-03-28 03:48 am (UTC)Repercussions by crazy_obsessed (McShep)
http://crazy-obsessed.livejournal.com/9248.html
Finding Home by Diamond-Raven (McShep, back in Atlantis later)
http://sgabigbang.talkoncorners.net/?view=fic&id=37
The Sentinels of Atlantis verse by Keira Marcos (McShep)
http://keiramarcos.com/fan-fiction/stargate-atlantis-fan-fiction/the-sentinels-of-atlantis-atlantissentinel/
Into the Whirlwind by slybrarian (Sheppard/Lorne)
http://www.wraithbait.com/viewstory.php?sid=14053&index=1
And as a bonus:
Evil Overlord Sheppard by GraceandFire
https://archiveofourown.org/series/2541
AU: Sheppard is not in charge of Atlantis, but in charge of his own planet.