*Spoilers for Season 9*: In “Avalon Part 1� (s09e01), I’ve always been intrigued by Sam’s comment to Mitchell about her “having her reasons" for wanting the Area 51 job. Aside from the fact that AT was on maternity leave for the first few months of season 9, I’ve always liked to believe that in terms of the characters’ storylines, this was another innuendo about Sam’s relationship with Jack. So this story takes on how they might have come to an “understanding� in the months between seasons 8 and 9.

Set before the season 9 opener “Avalon." Note that in this timeline, Sam’s been at Area 51 for a little bit longer than just a week (something like 3 or 4 weeks) and Jack’s been at the Pentagon for a little bit longer than that (say a couple of months).