This is tough to answer because there are SO MANY amazing fics in this fandom!
Personally, my favorite fics are the ones that really make me think, make me question everything. I tend to be partial to old school fics and I’ll try to rec some that I haven’t seen mentioned a bunch of times.
I rec’d The Other Man yesterday. It is one of my all time favorites because it forces you to question everything. Another fic like this is Pentimento. Be ready for some serious recovery after these.
Blinded by White Light is up there. It’s one of my favorite Post-Colonization fics because it is so different. dashakay was nice enough to answer me yesterday about the origins of the idea behind it all. Check out her response after you read it!
Those three are pretty heavy, so I’ll give you a couple lighter ones.
I Have Known A Boy Named Fox and a Man Named Mulder isn’t mentioned often. Mulder gets rushed to the hospital and regresses in age. Scully has to care for him as he ages up again from 3 years old. It is fascinating.
The last one I’ll rec for now is novel length. Erlona’s Heart has Mulder and Scully shipwrecked on an island while Scully battles cancer. There is a mystery to this island, with mist and backstory.
I’ve read so many great fics over the last 21 years, I’d be happy to rec more any time you like, anon!
Happy Reading :)