Kids in these fics have Scully or Mulder, or Doggett or Reyes as parents. These are just kids from deliberate relationships, ftr.

Other is an Original Character

Scully

Air Conditioning by Acidrain23
Bathrooms and Other Benefits by Sara B
Bathrooms and Other Benefits 2: More Benefits by Sara B
Bathrooms and Other Benefits 3: Beneficial Dividends by Sara B
Birth Day by Siobhan Gormley
Breathe by Terri
Could've Been RogueAngel
Daddy by Grey Woman
The Devotion Series by Sarah, Sophia, Quetzel, and Lady X
If by Ewa
If Only I by Ewa
In One Day by LJP
The Long Trail Home by Nantglyn
Moms Only Chat by Megan
A Mother's Secrets by Chrissie
Portrait of a Family by Lilith
Seed by Cathey Scully
Surprise by Chloe Durlem
Tangled by Kristy Anderson
Whatever We Become (Seed II) by Cathey Scully
A Wonderful Life part 1 part 2 by Donna

Mulder

Angie series by X FireLady
Annabelle Series Elizabeth L. Iacono
Children by Alicia Ann
The Dangerous Side Effects of Body Switching by Jeri
David part one by part two by Gerry Hill
Daughter of Mine by bellefleur
Dogged Determination III - Pandora's Box by Rhondda Lake
Dogged Determination IV - Suffer The Children by Rhondda Lake
Dogged Determination Interlude IV - Endless Knot by Rhondda Lake
Dogged Determination V - Watched Over by Rhondda Lake
Four Corners Cycle by Spookey247
The Girl With My Sister's Face by Henle Girl
Jurassic Files by Bruce C and Angelia D
Killing Season by Sharon Harkins-Murphy
Katelyn I. Family by Toma
Katelyn II. The Return of Trouble by Toma and Kelley E. Kelly
The Long Trail Home by Nantglyn
Lost Child by Amperage
Lost Childhood by Shorts
Marry Our Fortunes by Alicia K
Megan by Gilly-Bean
Megan II: I Don't Know by Gilly-Bean
Moms Only Chat by Megan
Once Upon a Time: Welcome Home by Meaghan McScully
Once Upon a Time: Against All Odds by Meaghan McScully
Once Upon A Time: Reunited by Meaghan McScully
Only Because He Needed Us and Broken Mosaic by Neoxphile
Promises by Phenyx
Sarah series by Carol Gritton and Co.
Sarah by Mystic Kat
Second Chance by SupernaturalAngel
Tangency by Heather B
Trust series by Parrotfish
The White Picket Fences Series by Batela (also m/m slash)

Skinner

Anthony: book one by Clare Skinner
Anthony: book two by Clare Skinner
Anthony: book three by Clare Skinner
Anthony: book four by Clare Skinner
Anthony: book five by Clare Skinner
O Holy Night by Bonnie Drew
Peaceful, Easy Feeling by Bonnie Drew
Father's Day by Bonnie Drew
A Quarter Past Three by Bonnie Drew
Downtime by Bonnie Drew
Seasons series by Jude Dettmann
Walter and Mariel series by Mary Mastrangelo

Doggett

Sarah by Mystic Kat
Snow and Mistletoe by Neoxphile

Krycek

If Alex Fell series by Frohike

Frohike or Langly or Byers

Elyssa by Mandi Krueger

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Scully/Skinner

Adopted Son by Kel
...and Baby Makes Six! by Skinner's Vieja
After William by Philiater
Archangel by Philiater
The Crouching Thing by Sarah Ellen Parsons
It's Only Ever Been You by kimo-sabe
Greatest Gift of All by Kris
Love and Lovers by Donna
November Eleventh by Lisby
Offspring part 1 pt 2 pt 3 pt 4 pt 5 by Deslea R. Judd
The Reoccurring Nightmare III - Cheating Fate by Lady Disdain
Wonderland Lodge by Kristen
A Wonderland Life by Kristen
A Wonderland Life 2 by Kristen

Scully/Doggett

Draw Down the Moon by Jenna Tooms
Happy Girl by MainerIA
Heartsong: The Best of Friends by Julie L. Jekel
They're Here 2 by L. M. Shard
They're Here 3 by L. M. Shard

Scully/Krycek

Baby Girl by Nadia S.
Buttons by Nadia S
The Cocktail Party by Nadia S
Dana's Desires 1 - Krycek by Nadia S
Dana's Desires 2 - Doggett by Nadia S
Dana's Desires 3 - Skinner by Nadia S
Deduction Seduction by Nadia S.
Doggett's Investigation by Nadia S
Doggett's Report by Nadia S
Finding The Past by Bleachy-nii
The Island of X by Tammy D. Aiken-Phillips
Krycek Bites the Bullet by Nadia S
Krycek's Headache by Nadia S
The Long and Winding Road by Abbey R
One Last Time by Jennifer Cuzzo
The Ratling 1: Swollen Ankles by Tara Leigh Thorne
The Ratling 2: Ambush by Tara Leigh Thorne
The Ratling 3: Bad Coffee by Tara Leigh Thorne
The Ratling 4: Comparing The Martyrs by Tara Leigh Thorne
Rocking The Cradle by Jennifer Cuzzo
Secrets by Jennifer Cuzzo
Surviving by Jennifer Cuzzo
Three Men by Nadia S
Turning the Tables by Nadia S
Will by Helen B

Scully/Pendrell

Every Step 1: Just You by JayJay
Every Step 2: More Than I Could Ask For I by JayJay
Every Step 2: More than I can ask for 2 by JayJay

Mulder/Phoebe

Mulder/Diana

Mulder/Reyes

Mulder/Marita

Doggett/Samantha

Krycek/Missy

Krycek/Samantha

Day Becomes Night Day Becomes Night by Jamie Tanquary
Mrs. Krycek by Xanthe

Missy/Pendrell

Super Sunday by Angela W.
Undercover Operation Angela W

Skinner/Reyes

Skinner/Kim Cook

Skinner/Maggie Scully

Slash-y Other fics

Chosen One by Peach

Kitten by Amazon X  
Kitten II by Amazon X  
Life From the Ashes by Jo B
Life's Little Quirks... by Nikita
The Long and Winding Road by Kassandra
No Greater Gift by KinkyGrrl Diane
Pregnant Mulder by Bertie
Something in the Air by Claire Dobbins
Sympathy Pains by Bernice
Time of Your Life by Emerald Starburst
Too Blunt An Instrument by Rose Campion
Trust, Love, and Happiness, Too by Nikita
Vows by Ursula
We'll Be Okay by MFLuder
What We Need Right Now is Trust by Nikita

There's a Nursery Files challenge on this topic too, so if you'd like to write a fic about characters having kids with others go here for challenge details.