Pray With Me
This is a fill-in-the-blanks fic. It starts with the moment I think Scully starts to think about motherhood again. I placed that happening after Milagro for reasons you will see in the text and ends before Nothing important happened today I. I rearranged the timeline of the episodes in a way I think it makes sense story wise based on the characters dialogue and behavior.
In this text my order is; Milagro, Biogenesis-The Sixth Extinction-Amor Fati,(Per Manum flashbacks), The Unnatural, Three of a kind, Field Trip, Hungry, Millenium, Sein und Zeit, Closure, all things, Rush, Fight Club, Hollywood A.D. The rest of the episodes are the season's order. My reasoning is that in The Unnatural Mulder jokes with Scully about her problems, including her biological clock. Now Mulder can be daft but this is a cruel comment to make given that he knows Scully is barren, but if she asked him to be the sperm donor after Milagro and they are doing the preparations the joke makes sense: Both are hopeful the procedure will work. Then the trilogy has to have happened before the petition too, because IMO Mulder wouldn't dream of a family with Diana if he and Scully were already talking about that even if it didn't take in the end. The dream was about fixing all his loved ones lives and that would include Scully being able to have a child.