These alternate reality fics are written as if season 9 didn't happen.
The 13th Sign by Prufrock's Love
After William
I-IV by Susan
Al Dente by Spookey247
Annual Growth by Norma
Arms Wide
Open bellefleur
Ballgame by Cathey Scully
Babysitting by Tabby
Cats and Cross-dressers by beduini
A Cold Night by Girlie_girl7
Decisions and
Consequences by xphilernj
Draw Down the Moon by Jenna Tooms (Doggett/Scully)
the Everything series by Eral C
First Steps series: I Le Lait
II Techicolor
III Peach Fuzz
IV The Necklace
V Fresh Air by Alanna
The G-Man's Guide To Post-Partum Sex by alanna
Good Mornings by Tabby
Hurricane Season by beduini and rah
I've Known Them For A Lifetime by little Starbuck*
My Favorite Day by Mish
OB-GYN by Girlie_girl7
On the Road Again by FoxfireX and Girlie Girl7
Party of Three series by Christine Leigh
Perfect Happiness by Lilxgirl
Priorities by Angel LeeAnn
Resuming by Norma
Starkweather series - season one by Scully3776 & SpookyKat
Scully, NORAD called... by dlynn
A Thousand Words by Menagerie
Two of a Kind by Girlie_girl7
The Unfinished Universe by Revely
You Should Be Proud by Faith N.