The Heart's Landscape (133K words, complete) by F.A. MacNeil
Fandom: X-Men & Alpha Flight
Rating: Teen and Up
Category: Gen, a very slow-burning M/M in the background
Characters: OCs, Alpha Flight team, Charles Xavier, Faiza Hussain, brief appearances by Jean Grey, Cyclops and Wolverine
Summary:
Canadian superheroes, or not. In Montreal, two small-time mutant activists contend with bureaucratic humiliations, government agents headhunting mutants for a new department, and a sketchy neurological research centre. What they discover isn't pretty.
This story is a re-imagining of Alpha Flight, but you really only need to be broadly familiar with the X-Men end of the Marvel universe to follow what's going on.
Read at AO3