I've got the required mods for it. No other ship mods installed.
And I wasn't paying attention to the battle, I just initiated and hit autopilot, which I wish I hadn't. I think it was Caeser's Legion..I have no idea.
I've now deleted my saved games, and started the game up. Still no way to start with Scy as a faction. Which I thought I could..and I don't really see them on the hyper space map either. Not that I exactly know if their system colours would change..
BUT the game codex shows the hulls and gun info. So it clearly loaded the files for that.