That's the good news. The bad news is there's some really dodgy content in "Gender Bender." After reading through a good half dozen reviews, the only TV critic who was willing (or able?) to focus on the story in view of its cultural context is Darren Mooney over at the m0vie blog.
To be fair to writers Larry and Paul Barber, their mess of a script contains a rake of fascinating ideas – even if it’s never entirely sure what to do with those ideas. Gender Bender doesn’t really work as a story, but it’s infinitely fascinating as a collection of nineties anxieties. From the opening scene in the rave club, Gender Bender feels very much of its time – an artifact of the early nineties, a capsule containing a whole host of uncertainties and insecurities.
His review is more insightful than anything I could manage. You should read it. In fact, you should go read them all. He's in the middle of season six. The X-Files: Gender Bender (Review)
Because the episode is focused on sex, unsurprisingly most of the post-eps are about sex. My problem with every fic, including these two, is that no one wanted to deal with the issue of consent. Here's a typical summary: "Scully is still feeling the effects of the brethren. Mulder helps her through it. Smut ensues." I don't want to sound like I'm judging anyone, but, personally, I find the idea of Mulder having sex with Scully while she's clearly unable to consent to be a major turn-off. I don't even find it convincing as a premise. Sex pollen stories aren't sexy to me either, but at least the way that trope is generally written, it's obvious that no one is consenting. On the other hand, the spoiler section at Gossamer for "Gender Bender" could have just what you're looking for in fic. If so, knock yourself out.
Clay by Brighid
Spoilers: Spoilers for "Gender Bender"
Summary: Scully and the Last Temptation
What works in this story is Brighid's clever backstory for the Kindred, and her vivid use of language. The Last Temptation of Scully sections fall flat for me. However, her story about the Kindred made a lot more sense than the episode itself.
Second Thoughts by bardsmaid
Classification: Vignette, 155 words
Summary: Home safely from their encounter with The Kindred, Scully puzzles over what happened.
What the summary says. It doesn't address consent, but at least it doesn't turn Scully nearly being raped into an excuse for porn. It makes it clear how disturbing this case must have been for Scully, and it's only 155 words. Bravo, Bardsmaid.