Title: The Heart's Landscape
Author: F.A. MacNeil
Summary: Joel and his friend Paul run a Catholic Worker house for homeless mutants in Montreal. When they meet Jean-Paul and Jeanne-Marie Beaubier, who are offered suspicious work with the Canadian government, Joel and his friends become embroiled in a system that may not be as benevolent to mutants as it appears. A political story with elements of medical mystery and queer romance.
Fandom: You could consider this original fiction taking place in the X-Men univervse. Which one? Uhh. There's heavy borrowing from Alpha Flight vol. 2 and light thievery from Ultimate X-Men. The X-Men movieverse is now such a canon jigsaw puzzle that I give up on trying to situate anything there. It might fit with the current Marvel Cinematic Universe if you squint.
Status: Six chapters of a projected twenty completed. (54K words so far.)
So there are a lot of original characters, but familiar faces as well: Jean-Paul and Aurora, obviously, Heather and Jim Hudson, Walter Langkowski, Kyle Gibney/Wildchild, etc. It is a sequel, and reading The Aphanes first may answer some questions about the characters, but otherwise I think it stands on its own.