Archive of Our Own is the clear winner now. The tagging system means you can filter exactly what you want—post-'I Want to Believe' fix-its, weird casefic that reads like a lost episode, established relationship fluff. The quality bar is generally high because the kudos system surfaces the good stuff. I'd avoid Wattpad for this fandom; it skews way too young and the plots get... unhinged in a not-fun way. FF.net has a huge archive but it's messy to navigate and a lot of authors have migrated. Stick with AO3, sort by kudos or bookmarks, and you really can't go wrong.
Tumblr. Seriously. A lot of writers draft and share shorter pieces there, and the reblog chains lead you to amazing, under-the-radar longer works hosted on AO3 or Google Docs. The visual culture adds a whole other layer—moodboards, gif sets, fanart paired with fic. You find stories through vibes, not just tags.
Honestly? The best X-Files fanfiction I've ever read wasn't on a major archive. It was a multi-chapter casefic shared via a Yahoo! Group in the early 2000s, and I only found it because an author I liked mentioned it in her bio. That's the thing—this fandom has deep roots. You have to dig. Check the links sections on dedicated fansites, or even the TV Tropes fanfic recs page. Sometimes the most brilliant stories are hosted on someone's ancient Angelfire site, holding on by a digital thread.
I'm also partial to stories that play with the show's mytharc in clever ways, and those often pop up in smaller, curated collections. There's a LiveJournal community called 'xfilesfiction' that's semi-active, but its back catalog is a goldmine of tightly written, beta-read work. The comment sections there often have lively debates about characterization, which is a good sign the writing is taken seriously. It feels more like a community of peers than a content feed.
so maybe I'm sentimental, but the old archives hold up. The Gossamer site is still online and it's like walking through a museum—tons of stories from the '90s where the tech is hilariously dated but the angst is timeless. That said, I'm not convinced the 'best' stuff is all clustered on one modern platform. AO3 obviously has volume, but the sheer number of tags can bury the truly great character studies under a mountain of tropes.
My weird tip? Search for authors who wrote during the original run and see if they cross-posted to newer sites. A lot of them did, bringing that grounded, pre-movie-season-series-finale-disappointment energy. The characterization feels sharper, less influenced by later retcons. Sometimes the best finds are in the comments of old LiveJournal communities, where someone will link to a personal site that's still up.
I just reread a Mulder/Scully slow burn from 1998 last week that had better tension than most novels on my shelf. So maybe 'best' is less about where you look and more about when the story was written.
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I'm always struck by how often Mulder and Scully end up in 'Supernatural.' It's almost a rite of passage. The shared monster-of-the-week structure makes it seamless, but the real draw is throwing the ultimate skeptics into a world where the rules are openly supernatural. Watching Scully try to rationalize a ghost Sam and Dean are exorcising, or Mulder getting way too excited about a real vampire, writes itself. It's less about the lore crossover and more about that brilliant culture clash between FBI procedure and the Winchesters' 'salt and burn' method.
Another big one I've seen is with 'Twin Peaks.' Both shows have that core weirdness buried in small-town America, and the FBI connection is a natural bridge. A plot where Mulder gets obsessed with the Black Lodge while Scully tries to pin down a logical explanation for Laura Palmer's death just fits. The tone matches perfectly—that eerie, slow-burn mystery with a hint of cosmic horror. Those stories often lean into the psychological thriller side more than the sci-fi.
Weird thing is, I drifted away from 'X-Files' fic for years then came back and the landscape shifted. Instead of just UST and monster-of-week AUs, there's this whole subgenre now that treats their dynamic like a decades-long archaeological dig. Saw one recently set in 2015 where a retired Scully finds Mulder's old field notes with little doodles of her in the margins from 1993, and the whole story is her piecing together his side of their early years through these artifacts. It's less about will-they-won't-they and more about the sheer weight of shared history, the ways they documented each other even when they couldn't articulate it.
That approach feels truer to the show's later seasons to me. The fic that sticks now acknowledges the baggage—the loss, the lies, the institutional betrayal—but uses it as texture rather than just angst fodder. Their dynamic becomes about two people who have the same reference points for 'weird' and 'traumatic,' which is its own form of intimacy. You can't replicate that with any other pairing.
Archive of Our Own is basically the main hub for it now. I check there almost daily and new Mulder/Scully fics pop up constantly, plus a surprising amount of Krycek-centric stuff and monster-of-the-week episode tags. The tagging system is a lifesaver for finding post-revival seasons 10-11 content or sticking to the classic 90s vibe.
For a more curated, almost museum-like feel, sometimes I wander over to Gossamer. It's an old-school dedicated X-Files archive, so updates are slower, but the stories there feel like they have a different texture—authors who've been writing since the show first aired. You won't find the latest speculative fic about a new season there, but the depth on characters like the Lone Gunmen is unmatched.
My weird little tip is to search the X-Files tag on Dreamwidth. A lot of writers use it as a blogging platform to post snippets, headcanons, and link to their AO3 works, and the community circles there often signal-boost new stories you might miss otherwise.