It says in the walkthrough that you can't change who you're allied with after the initial choice, so I think this has messed up my storyline. I appear to have done all the side quests for the Shadow Runners, and haven't yet faced a boss.
This is a fantastic game, I've had over 3 years of enjoyment from it. Unfortunately the devs are pretty much no longer working on it, which means the playerbase is smaller than ever.
So a note to new players: stick at it! We all value your participation.