Somehow Sheppard goes back in time with no way back to the present. Either through accident or on purpose is up in the air but is (I think) obviously important because it gives the starting point for his frame of mind for the rest of the story.
When he arrives in the past the planet he's on is transformed from tents and horse drawn wagons into a planet that has some serious technology. He knows that he can't return to the present so he goes about setting up a new life on this world. When word of the Wraith awaking is released to the people of that world, Sheppard volunteers for their military, giving them a brief overview of his experience they put on one of their spaceships.
After the wraith come, despite their best efforts the planet is pretty much decimated and there are only a half dozen flight worthy spaceships left after they were ordered to retreat when it was realized there was no way to win. One of them is the ship that Sheppard is now in command of (he's in command either because the fight has been going on for quite some time and he rose in the ranks or through circumstances similar to what happened at the beginning of SGA and he'd proven himself to the crew and he was put in charge). The remains of the government on that world is in over its head and the commanders of each of the spaceships band together under Sheppard and the idea (he was listening, and drinking rotgut alcohol, to a broadcast of the government officials arguing over what to do before the Wraith return and remembers Larrin and the Travelers) to take as many people off the planet as they can and make it impossible for the Wraith to find them. After lots of arguing and finally Sheppard saying screw it because more people are going to die, he essentially takes the ships with anyone who wanted to come with them that they could safely fit. The ships take off and become a self-contained society. Sheppard steps down as ship's commander after its decided that the ones in charge of the ships are the ones that are going to be the ruling committee.
How the government is set up is really up the writer who is brave enough to take this on. I'm personally not going to touch it because it involves some serious ability in world building (and setting up new governments.) I just see that a little while after The Travelers are "born", Sheppard steps down from being in command and essentially rests.
This can be gen or shippy (whatever pairing that floats your boat) with some angsty man!pain or Sheppard isn't stuck back in time all alone and his best beloved is there with him (to argue with and fight beside). Hell, you can make it Sheppard/gun (Ronon-type) if you want to have him discover the origins of that gun he's lusted after since he saw it. *g*
(I hope this makes sense because sometimes I get rambly ideas that only seem good to me.)
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