Mulder as a single dad. In some fics Scully has died, and in others she's just not with him for one reason or another. Some of the ones she's alive in end in MSR, others don't.

All the Little Pieces She Left by Sarah Kiley
All These Changes by JEn
Angels Instead by conspiracy
Believe by L. Phillips
Broken Mosaic by Neoxphile
Butterfly Kiss by Diana Rubenstein
A Different Path by PamelaST
Emily Returns I-IV by Jessica Hildbold
Every Single Day by Angela CJ W.
The Four Corners Cycle by Spookey247
A Gauntlet and a Gift by Leslie Sholly
Gift Of Hope by Kristyn Collins
Goodbye My Lover by xXx Allison Janney Fan xXx
In the Clearing by Rae Lynn
Iolokus by MustangSally & Rivka T
Irreplaceable by Rachel West
Living Ever After Awsomeo Fox
Me, Sam by Hardra61
Me, Sam II by Hardra61
No Room For Tears by Hardra61
Our Princess by Debbie Cullen
Promises by Phenyx
Respects by Falconer
Running Leasons by MaybeAmanda and Spookey247
Through Perversity by Joann Humby
The Time For Miracles by Carol Gritton
The Wasteland by prufrock's love
We Who Remain Carry On by Neoxphile (wip)
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