I read it probably 15 years ago (1998-2002), while in college. It was on a website devoted to fanfic, but might have originated on the FFML (FanFiction Mailing List). It started with Rahne being trained by Wolverine in the Danger Room shortly after the whole Genosha mutate thing (she was struggling with feral impulses). He complains that she is not aggressive enough. She disembowels him to show that she can be aggressive, but she is afraid of what she might do if her temper gets away from her.
Somehow, they get yanked off to Limbo and have to rely on each other to survive, including the obligatory "confront your corrupted future selves" bit, which I'm pretty sure involved techno-organic virus corruption as with the Phalanx. Rahne has a Bible tucked into her underwear (I remember commenting to the author that it struck me as contrived and he admitted that was the only place he could think of her having it in her uniform) and over the course of the story, she converts Wolverine to Christianity. I think he died at the end in a heroic sacrifice to get Rahne back.
I'm pretty sure there was some sort of Autumnal theme to the story's title like "Falling Leaves". The website had images of Fall leaves. I want to say the website had a black background.