The idea:
Alternate Season 1 (possibly more) - they arrive in Atlantis, it start the same (ie everything in the first episode is right to a point) and then after that things go horribly wrong and somehow, they fail and have to abandon the city. No contact with earth, all their equipment and supplies with them and the help of the Athosians they have to live on a whole other planet, find their own food and set up their own way of living. At the same time, Elizabeth and John have to work out what their relation is now and could be later as Elizabeth got pregnant on a one night stand a few days before leaving for the city.
How the writting works:
My idea on having a partner on this one would be that we pick a character (ie you write John, I write Elizabeth) and we bander back between each other - do the whole story just from those two points of view.
Larkin writting Elizabeth.
Nicole writting John.
The Details:
The one night stand happens 2 or 3 days before they leave for Atlantis. Elizabeth visits John in his hotel/base room to finalise a few things on his joining the team and it turns into a one night stand (written from Elizabeth's POV and a Flashback).
Elizabeth's relationship with Simon - they've been trying for a baby while they are engaged, but after a year emotions are running high and still no baby. Things aren't going very well between them, so she takes the expedition assignment.
John's relationship with his dad - some argument when he was younger pushed him to join the air force to esacpe his father. Though now he disapproves of that so John can't win. He takes a trip to visit his dad before joining the expedition and leaving very annoyed at his father John seeks out Elizabeth to join the expedition. (One night stand).
On Atlantis, things go wrong with the shields, they fail early and the city is abandoned. A few people are lost in the evacuation and Elizabeth barely makes it through. They go to Athos.
On Athos, John and team are in the middle, or after a Wraith attack. John is left, Sumner and Tayla taken by the Wraith.
When they both meet up they explore the ancient city and collect a few jumpers – but they can't remain on the Athosian planet for some reason (currently unknown). So they leave to an address miss-dialled by Jinto and end up on what seems to be an abandoned or empty planet (more on that later)
Story starts in the middle of the evacuation, Elizabeth on Atlantis, John on Athos. There is no failsafe for the city so it doesn't rise – instead the city becomes flooded.
Earth is never contacted and will never find them (probably).
Characterization and Canon are kept as much as possible with the changes we are making to the original storyline.