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I've broken the stories up by what season they're set in, and then I specify the prompt and the genre! Unless specified otherwise, I think these are all canon-compliant.
If anything doesn't work, please let me know!
Pre-Series
Season One
Dust - One word prompt, Mulder hitting on Scully after someone insults her. Fluff.
Season Two
Season Three
"You're more than that" - Scully reassures Mulder after hearing people make fun of him. Hurt/Comfort.
Hug - "You look like you could use a hug." Hurt/Comfort.
Navel Piercing - "Do you have any piercings?"
Have you ever... - A tired Scully asks Mulder if he's ever had sex with a man and he returns the question in kind.
Oversized Scrubs - It was just something he’d gotten used to over the past few years of working with her. If Scully was doing an autopsy, chances were, he’d accidentally get a clear shot down her shirt. Light Hurt/Comfort, light angst
Season Four
Cold - One word prompt, Scully can't get warm. Angst.
Fine - Scully thinks Mulder's been overstepping while trying to find out if she's okay. Angst.
Obfuscated Frustration - During a tense day, Mulder accidentally makes Scully cry. Angst, hurt/comfort.
Season Five
Lisp - "Mulder brings attention to the fact Scully has a teeny-tiny lisp." Fluff, slight hurt/comfort.
Personality Quiz - Mulder asks Scully questions from a personality quiz during their drive and gets a little more than he bargained for. Reference to "Never Again."
"You're Satan" - Mulder sees a drunk Scully in her Halloween costume the first Halloween after her cancer. Fluff with a hint of angst.
Fight the Future
Season Six
Hit - Mulder accidentally hits Scully. Fluff, hurt/comfort.
Season Seven
Slow - One word prompt, their first time. Soft Smut.
Sunrise - One word prompt, morning sex. Soft Smut (I tried to be artistic, look away).
Hanky Panky - Pre-relationship Mulder and Scully get frisky on her couch, but both are too nervous to admit what's happening. Smutty.
Dom Mulder - Mulder finds out Scully likes a bit of domination in the bedroom. Smut
Stripes - One word prompt, Mulder admires his post-sex Scully marks on his back. Referenced Smut.
Jealousy + Drinking = Misunderstanding - "Shouldn't you be with him/her" + "You've been drinking tonight, haven't you". Fluff.
Raspberry Swirl - "Mulder rubbing Scully’s clit while he kisses her cheek and whispers filthy things in her ear." Smut.
Cuddle - The first time Scully asks Mulder to cuddle in their new, intimate relationship. Fluff.
Dom Scully - Scully teases Mulder during sex. Smut.
Meeting with Skinner - Mulder and Scully get a complaint about their "unprofessionalism." Humor, referenced smut.
Spending the Night - Scully finally decides she wants to stay the night. Fluff, romance, references to smut.
Breathe - "I feel like I can't breathe." Mulder comforts Scully when she has a panic attack. Angst, hurt/comfort, post-"Orison."
Dirty Talk - "What words do you like to hear during sex?" Smut.
Pussy - "Mulder tells Scully she has a beautiful pussy." Smut.
Office Jealousy - (pre-relationship) Scully gets jealous and Mulder assures her there's no competition.
Something Sweet - (pre-relationship) Scully gives Mulder a sweet present. Fluff.
Last time you felt jealous? - (pre-relationship) Mulder admits he's a little territorial of Scully. Fluff, ust.
Tip Toes and Bent Necks- A soft morning with Mulder and Scully. Fluff.
Season Eight
Grief Sex - Scully seeks out comfort. He just wants to be there for her. Smut and Angst.
Season Nine
Mourning - Doggett comforts Scully after she gave up William. "You can't sit there all day." Angst.
On The Run
Post-On The Run; Pre-IWTB
Dark Conversation - Mulder and Scully talk about their suicidal ideation. Angst. TW/Suicidal Thoughts.
I Want to Believe
Post-IWTB; Pre-Revival
Season Ten
Season Eleven
Post-Series
Original Series | Unspecified Season
Pinned - "I want to see you try to write a problematic Mulder: Scully does something risky and later they fight, resulting in Mulder pinning Scully down on the ground." Angst. Not really Canon-Compliant.
Contest - (pre-relationship) "How long can you just kiss before your hands start to wander?" and "What is your definition of having sex?" UST-y. Not really Canon-Compliant.
Radio Contest - (pre-relationship) Scully hears Mulder call into a radio station and he has to answer the question: "What's the sexiest thing someone could do for/to you?" Fluff, romance. Not Canon-Compliant.
Eyeful - (pre-relationship) Scully's stuck in a traffic jam and spills coffee on herself. She changes without realizing Mulder was in the car next to her, in full view.
Sing - Scully can't remember the name of a song and Mulder makes her sing to him so he can 'help' her.
More Lingerie - (multi-season) A continuation of my fic "Lingerie" where Mulder sees Scully in various states of undress.
Catcalling - (any season) Mulder witnesses Scully getting catcalled for the first time.
Advice - (any season, pre-relationship) Someone asks Mulder and Scully for romance advice. Fluff.