The Atlantis Expedition never knew Major Sheppard. When they arrive in the Pegasus Galaxy, however, they discover a single Ancient remained behind to protect the city.
His name is Iohannes Ianideus Licinus Pastor, but mostly they just call him John Sheppard...
A series of roughly canon-compliant rewrites of Stargate: Atlantis' five seasons, based on the premise that John Sheppard is and always has been an Ancient. Part of the Locality universe.
Rating: ranges from PG to R, averages at PG-13
Warnings: character death (major and minor), language (this is the main one), SyFy violence and gore, sexual themes and content (mainly slash, with some het), homophobia, (attempted) non con, mature humour, use of alcohol.... Nothing you'd not expect to see in SGA itself, with slightly more fade-to-black.
Spoilers: This story series place between "Rising" and "Enemy at the Gates", but calls upon knowledge of all the series in the plot, characterizations, and use of certain background characters, primarily those in SG1 but a few from SGU.
Pairings: Ancient!John Sheppard/Rodney McKay (main); Evan Lorne/Radek Zelenka (secondary); Carson Beckett/Laura Cadman, Elizabeth Weir/Stephen Caldwell, Sam Carter/Jack O'Neill, Jeanne Miller/Kaleb Miller, Teyla Emmagen/Kanaan (background); mentions of past Ancient!John Sheppard/OFC, Elizabeth Weir/Simon Wallis, Stephen Caldwell/OFC, Evan Lorne/OFC, Jack O'Neill/Sarah O'Neill, and Janus/Everybody.
Disclaimer: I don't own these characters. I don't even own the humorous (and legally useless) disclaimer you're reading now.
Notes: Locality universe, but it is not necessary to read any of the other stories in that universe to understand these. Various notes for the series' can be found here.