These alternate reality fics are written as if seasons 8 & 9 didn't happen.
An Acceptable Level Of Happiness by Jenna Tooms
Coming Back To You by Marlen
Cunegund's Restoration, or, The Best of All Possible Worlds, Really by Livia
Don't Close Your Eyes Tonight by Keleka
Don't Close Your Eyes Tonight II by Keleka
Eyes of A Child by Lovesfox
Find The Future by xphilernj and Fibbie prologue, chapter 1, chapter 2, chapter 3, chapter 4
The Flick of a Switch by Aislinn Carter
The Fringe series by Michelle Kiefer (Fringe, Hearth, and Haven)
Glass Landscape by Annie Sewell-Jennings
Hearts and Bones
by Michelle Kiefer
Interstice by Christy
Inventing the Mulders by Prufrock's Love
Journey by Susan
The Lullaby series by Donnilee
One For the Road by Starbuck_Jayne
The Return by Grey Woman
Sara Mulder stories by Laura Means
Under Construction by MaybeAmanda
Womb For Revenge by Neoxphile
Way of the Cradle by Spooky's Girl