Scully and (usually) Mulder expecting a new bundle of joy.

Pre-Series

A Baby Changes Everything by piper maru duchovny
The Beginning of Love by Erin Blair
Connection by "Jayne Austin"
Connection II by "Jayne Austin"
I Shall Believe by Cathey Scully
A Simple Twist of Fate? by x-girl1
There You Were by allialli

Seasons 1-6
Some stories might go beyond season 6 but the first pregnancy, if there are multiple, occurs in seasons 1-6 in each story

Adam by Lyndal
After the Future by Donna
All That is Dark and Bright by Malibu Sunset
Archangel by Philiater
Assignment by Donna
Balance by Devin
Babysitting IV. Hi Em, It's Me by Binky
Babysitting V. Baby Shower by Binky
Babysitting VI. Home to My Sweethearts by Binky
Babysitting VII. Now We Are Four by Binky and Flowers By Irene
Bambino by Candy Cockrell
The Beach by Devin
Ben by Jess
Birth Day by Siobhan Gormley
Birth: Ocean by Jenrose
Breathe by Terri
The Butterfly Universe by bugs
Capitulation by Wylfcynne
The Child by Wintermoon
Chosen by Angela CJ W.
Chrysanthemum by Alethea Lynn
Chy an Dor by TRUTHWEBOTHKNOW1
Could've Been by RogueAngel
Daniel/The Couch series by MacSpooky and Ten
A Day In The Life Of Dana by Geri H
The Devotion Series by Sarah, Sophia, Quetzel, and Lady X
The Discovery Series by Erin Blair
Dogged Determination IV - Suffer The Children by Rhondda Lake
Dogged Determination V - Watched Over by Rhondda Lake
Domestic Inclinations by Gwinne
Dreams Come True by Ruth
Dreams Come True 02 by Ruth
Dreams Come True 03 by Ruth
Dreams Come True 04 by Ruth
Eloin by Annette Gisby
Ersatz Promises by Susanne Barringer and Suzanne Schramm (FYI - doesn't end happily)
Every Step 1: Just You by JayJay (agent Pendrell's baby)
The Family G-Man by Neoxphile and Felinefemme (a few pregnancies...)
A Favor for Scully by Scarlet Scully
Fondest Dream by Debbie Cullen
Fox and Dana series by Jo Ann Medrano
The Fruit of Our Labors by L M M
The Generations series by MacSpooky and Co.
Ghosts of Christmas Yet to Come by Tarin Z.

Season 7 (setbeforeRequiem)
Once-upon-a-time spoilerfic? Darn good guesses? Who knows. (fics that go entirely AU mid-Requiem go here too)

87 Shades of Black I-III by Slippin' Mickeys
...And So It Begins by Montana1416
Baby Mine by Debbie Gramlich
Baby, Oh Baby! by Cassie Consten
Christmas Surprise: The Drive Home by Agent Leki
Conceptus Immaculus by Kathy E.
The Climb by Starbuck2824
Dark Seed by bugs
Deliverance From Evil by Jacquie LaVa and Tess
The Dream Series by Dream Cole
Equanimity by LuvTheBeez
Finally Home by Natalie Scully
Four is a Wonderful Number by Agent Leki
Futures by Donna
Healing Touches by Jayne Austin
Intimacy Deux by MoJo
Journal 2000 by MD1016
Landfall by Ambress
A Legacy by dlynn
Life On The Edge series by Kate Rickman
Miracle by Jinxd n cursed
Mystery by Tesla (pregnancy implied)
One Glimpse of His Eyes by nikki
Our First Christmas by jes88
Pater Familias by OneMillionAndNine
The Ratling 1: Swollen Ankles by Tara Leigh Thorne
Regrets and Resolutions by Paige Caldwell
Rocking The Cradle by Jennifer Cuzzo
Safe in Utah by Autumn
Scully's Choices by Mystphile
Second Birth by Alien Girl
Silent Night by aRcaDIaNFall$
Syadiloh by MustangSally and Rivka T
Surviving by Jennifer Cuzzo
Tidings by Ambress
This Fragile UniverseWIPby Neoxphile
An Unexpected Surprise by xphilernj
Unreasonable Facsimile by Deenalynn
Wishful Thinking by Caz the Beeslayer
Zoe series by Smurf

"Requiem" thru Season 8
aka canon pregnancy stories, though the baby often isn't a boy named William given many were written prior to Existence

40 Weeks by Malibu Sunset
Accolades by Becka F.
Across the Void by Zuffy
Ad Astra per Aspera by Charlotte Unsworth
After Mulder: I Making Circles by Kimberly
After Mulder: II Moving Mountains by Kimberly
All I Will Remember by Namarie
All of Life's Etceteras by Rae
All Of Her by Becka F.
All of These are Nothing by Luperkal
All Which It Inherit 3: Such Stuff As Dreams Are Made On by Brandon D. Ray
All Ye Faithful by Foxsong
Almost Family Series by Donna
Almost Home by Shoshana
Alone in a Crowded Heart by Tess
Alternatives by Donna
The Anomaly by Joann Humby, Aptmt42 and Medusa
And Baby Makes Three by Beautiful Evidence
An Answer to All Things by LJP
Anybody Miss Me? by Corran
Arms Wide Openbellefleur
As Darker Grows the Night by Leslie Sholly
At What Price by SpookyCC
Awakening by Donna
Axiom by little Starbuck*
Baby Girl by Nadia S.
The Baby Dance by Ericka D
Baby Steps by Gwinne
Battling Hearts, Crumbling Allegiances by Rockenpnay (DSR)
The Best Miracle by Jenna
Bethlehem, Pennsylvania by Dramaphile
Beyond Alternatives by Donna
Birth by TeeTee
Bitter Pills by MaidenJedi
Bittersweet Renaissance by Caroline
Black and White Make Red by Jenna Tooms
Blue Eyes Behind Gray Bars by RLO
Breathe by Gwinne
Breathe by Miranda
Breathing by Jamie Greco
Buttons by Nadia S (Krycek's baby)
By Falling In And In by Aloysia Virgata
The Caretakers by Kelly Keil
Catching Up by loveJanick
the Changed series by Cathey Scully
Chasing Shadows by Entil'zha
Cherokee by Rachel Wilder
Child of Mine by Ally
Chosen One by Cheri
Christmas Revelations by Jumella1
Christmas Spirit by Neoxphile
Christopher Ryan Scully series by Jori
Closure by Kyouryoku Senshi
The Cocktail Party by Nadia S (Krycek's baby)
Consolation by Angela W.
Consolation by Kyouryoku Senshi
Contemplating The Unbelievable by Ewa
Cunegund's Restoration, or, The Best of All Possible Worlds, Really by Livia
The Cure by jawsoxz3
Cursing Miracles I by ElizabethAnn
Daddy by Angela W (password is "avalanche")
Dana's Desires 1 - Krycek by Nadia S (Krycek's baby)
Dana's Desires 2 - Doggett by Nadia S (Krycek's baby)
Dana's Desires 3 - Skinner by Nadia S (Krycek's baby)
The Dance by DM
Darkness Returns by Sara B.
Daughter by Ducky's Dream
Day of Magic by Jacquie LaVa
Days Between by Kel
Dead Fish by Rachel Wilder
The Dead Months by TCS1121
Death's Door is Standing Wide Open by SkepticalScully
Deduction Seduction by Nadia S.
Deep Breath by Catherine M.
Deep Breathing by Scully221
Deep Breathing: 02. The Prodigal by Scully221
Delivering the News by Becka F
Delivery by Katriena Knights
Delivery at the Corner of Dupont and Connecticut by Rachel Wilder
Democrat Hot Springs by Donna
Dinner With Doggett by Nadia S.
Displaced by shawntaw
Do Believe by Debunker77
Doctor, Copper, Sailor, Corpse by Scarlet Baldy
Doggett's Investigation by Nadia S (Krycek's baby)
Doggett's Report by Nadia S (Krycek's baby)
Domestic Inclinations by Gwinne
Don't Give Up On Me by Kyouryoku Senshi
East Side of Eden by conspiracy
Eat Me, Drink Me by Maidenjedi
Eavesdropping by flynn
Eclipse by Diana Battis and alanna
Empathy by Kyouryoku Senshi
Empty by Sara B.
Empty Graves by Kathleen A
Endless Snow by Amy H
Enter Mulder by Cinnamon Scully
Etiolate by alanna
Everlasting Miracle by DScully141
Existessence by WildwingSuz
An Explanation by Gibber
Explanations by Angela W.
Eyes and Ears by Clarice89
Eyes of A Child by LovesFox
Facing Destiny by Kyouryoku Senshi
Faith by DKNYScully
Faith by T. Griffen
False Visions by Marlen
Family Matters by Devin
FBI Deliveryman by Pattie
Feathers by Bluesea
The Female of the Species by Wylfcynne
Finding the Gifts by Kathleen A
First Born by diamondlife17
First Day Back by shanno
First Response by Gwinne
Fish Listen - Together by Donna
The Flick of a Switch by Aislinn Carter
Found Faith and Lost Time by ML
The Fourth Wish by Neoxphile
Foreseeing Premonition by Andi Mitchell
Foux by alanna
The Fractured Landscape by Zuffy and Littljoe
Frisson by Kemystre
Frohike's Baby by Kristina
Fruition by Suzanne L. Feld
The G-man's Guide to Unemployment by alanna and Emma Brightman
Gabriel by Mish
Genesis by M. Edison
Getting Used To by Jen
The Gift by The Fox
The Ghost of You and Me by Blackwood
Ghosts by Megan C
Gifts by Kristel S. Oxley-Johns
The Girl With My Sister's Face by Henle Girl
Giving Everything They Have To Give by XSketch
Glass Landscape by Annie Sewell-Jennings
The Glimmering Girl by Tesla
Going Thru The Motions by Marlen
Graveside by Dryad
Great Expectations by bellefleur and Emily Sims
Guitar Hero by Alicia K.
Happily Ever After by XfileySR
Happy Girl by MainerIA
Healer by Deslea R. Judd
Healing by TrthIsOutThere
Heart Turned Inward by Keleka
Heartbeat by M. H. Greathouse
Hidden Gifts by Angel-Wings Gaskins
Hieroglyphs of Memory by Zuffy
His Child by Jaime Lyn
Holding the Pieces by Georgina M
Homecoming by savagemom
How I Told Him by Trekkie6
How She Told Me by Trekkie6
I Dream Of Her by Marlen
I Just Wanna Run by RLO
I Know What You Did... by Henle Girl
I Will Not Watch the Ocean by Katriena Knights
I'm Here by Kyouryoku Senshi
I'm Rubber, You're Glue by David S
If Wishes Were Horses by Annette Gisby
If You Believe by Anonymous and Lizzi
Immortal Innocence by annaK
ImpasseAgent L
Impossible Choices by Ally
Impressions by PD
In Darkness, Light by Kristel S. Oxley-Johns
In Rama, A Voice Was Heard by dlynn
In Rama 2. But Hope That is Seen by dlynn
In Rama 3. Day by Night and Night by Day by dlynn
In The End by SnickJF
In The Next Moment by Tissa
The Infinite Love Contained In One So Small by Angst
Innermost Pain by Donna
Intermission by Exley 61
Introspection: Return by Lauren and Jen
Is That Your Final Answer? by LJP
It's Me by Lee Burwasser
It's a Wonderful Abnormal Life by Spookyteacher
Jane by shippyphile
Journey by Susan
Joy Begets Sorrow by Parrotfish
Just Doing My Job by beduini
Kodomo Tame Ni by White Star 2
Krycek Bites the Bullet by Nadia S (Krycek's baby)
Krycek's Headache by Nadia S (Krycek's baby)
Labor Day by Justine L.
Laborious Exertions by Triton
Lament by Kyouryoku Senshi
Last Night by Spookyteacher
The Laws of Coming and Going by Buckingham
Legitimate by beduini
Lonely This Christmas by Lizzi W.
Long Lay the World by Bella Maria
Lost and Found by Sheryl D.
The Lullaby series by Donnilee
Lullaby Voice by PD
A Man Walks Into a Bar... by Agent L
The Marriage series by Angela W
Maternal Beauty by Kyouryoku Senshi
Midnight Wonders by Egyptian Princess of 1290 bc
Minya Minuet by Mish
Miracle by Ana H
Misconception by Christina
Missing the Gaze by mercury_999
Missing Time by Gwinne
Missing Time by Rachel Wilder
A More Perfect Fit by DM
More Questions by LJP
More Than The Clouds by Little Starbuck*
The Most Wonderful Time of the Year by sylvia
A Mother Always Knows by Rachel Wilder
Mulder's Son by jrfpatton
My Favorite Word by Mish
My Grown-Up Christmas Wish by Spooky152
My One True Love by Agent Leki
My Travels with Charley series by Windsinger
Mystery at St Mary Magdalene by Mary
Natalie by little Starbuck*
Neither Moon Nor Earth by Sabine
Never Give Up on a Miracle by Kyouryoku Senshi
The New Arrival by The Fox
A New Beginning by The Fox
A New Life by The Fox
The Night Before Christmas by Vickie Moseley
No Earthly Ships by Katriena Knights
Nothing Says Love Like Something From the Oven by RLO
Nova by Angel
Once Upon a Time: Against All Odds by Meaghan McScully
Once Upon A Time: Reunited by Meaghan McScully
One of the Good Guys by Jenna Tooms
One Last Answer by LJP
Ornamental by Pita1013
Our Baby by Kyouryoku Senshi
Our Existence by Devin
The Outer Senshi Files by Kyouryoku Senshi
Oxytocin by Ambress
Partners, Friends and Lovers by Wildafox
The Perfect Gift by Mulderache
A Place In The Cloud by Lady Disdain
Planting My Feet by Rachel Wilder
Prayers Fly Up by Windsinger
Pregnant Pause by Annette Gisby
Promise for the Future by Agent Diana Fowley
The Question by Kel
The Question II by Kel
Quis Custodiet by Lee Burwasser
Ready-Made Family by Kyouryoku Senshi
Recollections by C.T.S.
Reflection of the Truth by Erin Blair
Relax the Back, Breathe In, Breathe Out by Teliko. x3
Remorse by Kyouryoku Senshi
Return by L. C. Shipper
The Return by Philemom
Return to Me by LadyRaider
A Safe Place by Ana H
A Safe Place by LuvTheBeez
A Second Chance by Red0313
Sesame Street Days by VBjess
Sesame Street Days II by VBjess
Sesame Street Days by VBjess
Shadow of the Day by Egyptian Princess of 1290 bc
Shoulders by Missy J
Showdown at Casey's Bar and Grill by Katriena Knights
A Silence Full of Sounds by Emma Brightman
Skin Deep by Shoshana
The Sky is Broken by TH001
Snowman by BamaX
Someone Else's Child by ScullyJr2
Something Rational by agent myers
Something Rational 2. Won't Fear Love by agent myers
Something Rational 3.Taking You Home by agent myers
Something Rational 4. End The Struggle by agent myers
Special Delivery (or Bottom of the 9th, One Out) by B.F. Simon
Strawberries in Winter by Gina Rain
The Strength of Our Beliefs by Lynette
A Suitcase for the Moon by Snark
Sunset Visitation by mountainphile
Surprises by jawsoxz3
Survivors by lil gusty
Suspicions Abated by Autumn Fugazzi
Thank You For Coming Back to Us by Gillian
They're Here by L. M. Shard
A Thin Veneer by Analise
This is Happening by Donna
To Breathe Again by Maddict
Tree of Stars by Ericka D
Truly, Madly, Deeply by Jenna Tooms
Truth and Conflict 2: Apologia by Allronix
Turning the Tables by Nadia S (Krycek's baby)
Twins by Teetee
2,000,000 Seconds by Lindsay B
Unbroken Love by Kyouryoku Senshi
A Unique Creation by Lari R
Unmarried Mother by Halrloprillalar
Unspoken by Megan C
Unthinkable Things by Lisa
Velvet by Shipper M.D.
Visions of Significance by PGMT
Vulpecula by Jeri
Wait Until Your Father Gets Home by Lorri

We Believe by Anonymous and Lizzi
What to Expect When You're Babysitting by Jeri
When All The Stars Were Falling by Maidenjedi
when we are three by beduini
When You Died by Mickey
Where You Are by LoveFox42
Whispers from the Grave by Egyptian Princess of 1290 bc
Who Knew? by ElleThom
William was a Bullfrog by AgentMulderFox
Winter of Discontent by Teanna
Winter Nights by Emma Brightman
Wishing and Wanting by Starrlyte
With Me Always by Rachel Wilder
Woulda, Coulda, Shoulda by Kyouryoku Senshi
The Wrong Kind of Paradise by Martha
X Christmas Carol by SaraJ
X Is For Xenogenic by Donnilee
Xenophobia by Donnilee
Yesterdays by Starbuck_Jayne
You Are My Miracle by Whiskey Queen
You Are Not Alone by Keleka
You Can't Go Home Again by Leigh Alexander
You Come and Go Again by ML
Your Father Came Home by Lorri
Your Father's Child by Lorri
Zombies in a Newer Age by David Stoddard-Hunt
Zone of No Signal by Branwell

Season 9(ish)
After William by Philiater (Skinner's baby)
Draw Down the Moon by Jenna Tooms (Doggett's baby)
the Everything series by Eral C
The Family G-Man by Neoxphile and Felinefemme
My Favorite Day by Mish
Mysterious Ways by Neoxphile
The Reoccurring Nightmare II - Full Circle by Lady Disdain
The Second Miracle by Kyouryoku Senshi
Shopping For More Than A Tree by Katie Phillips
Terra Firma III: Per Ardua by Malibu Sunset
Terra Firma IV: Vita Nova by Malibu Sunset
They're Here 2 by L. M. Shard
They're Here 3 by L. M. Shard
Without You by Jennis524

Post-Series
Absolution by Tlynn
Adding to the Family by xfilesjunkie
After The Truth series by Pattie
Alethea by Kyouryoku Senshi
An Alternate Reality by Fatcat
And Baby Makes Four by gillian dana
Apocalyptic Eden by Kirsten Kerkhof
Bedtime Story by Philemom
Beyond the Blue by JHJ Armstrong
The Birds, The Bees and The Sunflower Seeds by DanaKMulderScully
Biting the Bullet by Starbuck_Jayne
The Burpday series by Kelly J. Thompson
Christmas Delight by Erin Blair
A Christmas Wish by Erin Blair
A Cold Night by Girlie_girl7
Crystalic Millennia by Kyouryoku Senshi
The Empty Chair by Sara B
Faith I: The Substance of Things Hoped For by Dawn
Faith II: Reservations for Two by Dawn
The Family Files by Wildafox0619

IWTB/Post-IWTB
fics specifically set during or post-movie

Another Chance by Kyouryoku Senshi
Destination: Truth by Kyouryoku Senshi and Billie Reid
Don't Give Up by Kyouryoku Senshi
The Family G-Man: IWTB by Neoxphile and Felinefemme
The Family G-Man: From Here to Paternity by Neoxphile and Felinefemme
Iunctio ut Redimio: Book 1 by Kay
Iunctio ut Redimio: Book 2 by Kay
Iunctus Liberi by Kation
The Next Case by Donna
Nine Months, One Day by devout2David
Out of Darkness by KS
Second Chances by Gillyfan
A Sleepy Little Town: Memory House by Neoxphile
The Truth, Then and Now by FatCat

seasons 10-11 Blessing by KS
End of the Road by KS
Everything in Its Place by Joelyjo
February 23rd, 2018 by KS
I'll Follow You Down by KS
Labor Day by kyouryokusenshi
The Visit by Kyouryoku Senshi

Alternate Reality
fics that have nothing to do with The X-Files, but feature Mulder and Scully anyway

Bathrooms and Other Benefits 3: Beneficial Dividends by Sara B
The Bet by Gillyfan
Coach II by Gillian Leigh
Just Fine by Rebel
The Long Trail Home by Nantglyn
Meant To Be II: Children by Jinxd n cursed
What I Want 6: Dance with Devils by LaurieAF
When Fate Takes A Hand by Madam F

Timeline Unspecified
AU stories without spoilers or dates to nail the timeframe

Afterseries by Joey R.
Baby Plans by Kristen
A Challenging Life by Billie Reid
Day Becomes Night Day Becomes Night by Jamie Tanquary
Pink Ribbon by The X-Filer
Saving Me by Egyptian Princess of 1290 bc

Ready for something different? Try the Pregnant Reyes and Pregnant Others lists next!

We could always use more new additions. Consider penning a fic for one of our pregnancy related challenges :)

Psst! Don't forget that babies and other children are welcomed additions to this year's Christmas challenge: the I'll Be Home for Christmas (If Only in My Dreams) Challenge.

Or, try one of the other challenges below:

• Baby/Kidfic plot Generator <-- several of the prompts are pregnancy related
• Outnumbered Challenge
• First Christmas With You Challenge
• Tell Mulder, Tell Mulder Challenge
• Lamaze Class Challenge
• One Each Way Challenge
• When The Wind Blows Challenge
• Mixed Feelings Challenge
• It's Another Boy Challenge
• Season Eight Missing Scenes Challenge Pack
• Christmas List Challenge
• Moving Day Challenge
• Big Family Challenge
• GillyX29's Birth Scene Challenge
• Merry Multiples Challenge