Complications Trilogy by Sarah Kiley

308,000 Words

Complications Cover

Complications: After Mulder is in a car accident, Scully continues her investigation in an effort to save him.

Second Chances: Four months after being arrested, Mulder breaks out of prison and seeks Scully's help in clearing his name. To do so, they must make a cross-country trip on the run from the law while Scully has second thoughts about marrying another man. Could this be Mulder and Scully's second chance?

Last Dance: Mulder's messing with something he shouldn't be.

This is an epic early story, beginning in Season 2, so it involves some characters  who never made it far into Season 3.  It's quite a complicated story, to match its name, as it involves time travel and parallel universes, which always make my head spin. It can get quite concerning MSR-wise at points, but you have to trust that they'll find a way.  But I admit to being very glad that an epilogue was added...

All covers are by Sarah.

 

Wish Series by viXen

39,000 Words

WIsh Series cover

THE WISH: On St. Patrick's Day, Scully is given the opportunity to see how life could be different had alternate paths been chosen.

THE WISH II: ALL THE COLORS: Mulder takes a drive that sends him on an unexpected journey.

THE WISH III: A DREAM IS A WISH:  Mulder and Scully face implications

Happy St Patrick's Day. I believe smut is the traditional  St Patrick's Day gift, so please enjoy.

Mobius by ShipperX (LA Ward)

50,000 Words

Mobius cover

While investigating the disappearance of a physicist, Scully finds someone she didn’t expect—Mulder.

This is a post-Requiem fic, with Scully working alone after Mulder's disappearance.   It's a very clever story about our agents and their fight to reunite.

Some very early visitors to this page may have noticed the change of cover - Once again, I stumbled across the original cover right after uploading the story here so I've replaced it in the files.  I assume this cover was made by the author but please let me know if you know otherwise. 🙂

All Hallow’s Eve series by Windsinger

192,000 Words

All Hallow's Eve cover
Part of the All Hallow's Eve series:

Driving back to Washington on Halloween evening Mulder and Scully see strange lights in the sky over rural Maryland, stop to investigate, and find themselves spending a night they will not soon forget.

This one started out fairly painlessly, but Sue pushed the angst up each year as she added a new volume and sucked us in further.  But wait, there's more! There's also a shorter story called "The Messenger" that works as an epilogue which I'll post separately as it fits into a few of the different universes that Windsinger was writing at the time.  (There's a Cliff's notes guide to all the series involved at the end of that fic so you can follow it without having to read every story. )

Messenger, The by Windsinger

10,000 Words

Messenger cover
Part of the All Hallow's Eve series:

In the midst of his unbearable suffering aboard the alien ship, Mulder reaches out and makes unexpected contact with an amazing ally. With the help of another old friend, the messenger sets forth. It's All Hallow's Eve and anything can happen.

This fic links together a few of the universes Windsinger was writing in.  It works as an epilogue to the All Hallow's Eve series, but it slots into the My Travels with Charley series and features Jake from her two Red Shoe Diary crossover fics, Jake's Luck and Jake and Fox Join the Club.

According to Windsinger "This is one weird story. I'm posting it as a stand- alone because I can't figure out what series to put it under. It's especially for the fans of my 'All Hallow's Eve' series which I 'finished' over two years ago. Consider this an epilogue. In fact it will probably make much more sense to them then to anyone. I'm also placing it as Chapter V of 'My Travels with Charley' series (a little something for Dana.) To make things even more confusing, Jake of my two-novel Jake series (Jake of Red Shoes Diaries) also makes an important appearance. To help out everyone -- even for those who have read everything but who need a refresher -- a synopsis of what you need to know about All Hallow's Eve, My Travels with Charley AND Jake are included at the end of chapter 2 of The Messenger. Just for fun -- try to figure it out by yourself first. I dare you....

Fumbling Towards Ecstasy by Jenna Tooms

51,000 Words

Book Cover: Fumbling Towards Ecstasy by Jenna Tooms

Scully comes to Mulder with a wound only he can heal.

Content Warning: non-con (past)

Fumbling Towards Ecstasy was a popular album by Sarah McLachlan back in the day. This time Jenna's used each track as inspiration for a chapter.  This one could be a little implausible, but the same could be said of at least 9/10 of all excuses for smut - plus if plausibility was a problem for you you wouldn't be watching the X-Files or reading its fanfic.  There's some hot monkey loving in Jenna's story, and Mulder is certainly enthusiastic to help.

If you're looking for Ryo Sen's angstfest of the same name, you can find it here.

Butterfly in China, A by Nicknoc

36,000 words

Book Cover: Butterfly in China, A by Nicknoc

Mulder and Scully slip into an alternate universe where they meet themselves living a happy life together.

 

After being forced to make out so as not to blow their cover, Mulder and Scully end up stuck in a situation that provides further temptation...

Quantum by Emma D

54,500 words

Book Cover: Quantum by Emma D

Is the grass really greener?

A big thank you to xphilernj for compiling this one.  It was originally posted to Ephemeral in around 2009 but missed being archived at Gossamer, and had to be laboriously put together from various sources following the Ephemeral glitch.   This is the first story in Emma's Quantum Universe.  Links to the other two stories, The Road Less Traveled and Falling, can be found below.

Old Growth Forest by Andrea

102,000 words

Book Cover: Old Growth Forest by Andrea
Editions:Original Version

While following up a case of disappearing homeless, Mulder and Scully are pulled into the mystery.

This is the revised/updated edition.

 

Patty has provided a link to the original version in the comments below. Thanks Patty.

I suggest ficsave.xyz if you'd like to download from fanfiction.net.

Cubed by Louise Marin

37,000 words

Book Cover: Cubed by Louise Marin

Scully does a little body-swapping of her own. Can she and Mulder make it back to each other? Do they want to?

Author's Note: This story takes place around the middle of season six, but splits off into its own universe sometime before the events of Two Fathers.

I found a second dustjacket for this one at annex-files.com

Annex cover - artist unknown. There looks like a signature but I can't identify it. 🙁