This came out of a what if session after I hit the end of Felix Iresso's companion quests on my sage. Purely speculative, of course, and likely to be overturned by whatever the writers have in store for the game story, but ah well. This story is predicated on Iresso's companion quests, so will have obvious and explicit spoilers for those. Where there are spoilers for the rest of the JC storyline, I will mark them.
Hope you enjoy!
Edit: Summary of Iresso's companion quests for those who haven't done them/need a refresher: