Yes, I took a whack at PSOep3 and while I've mostly been testing than actually playing, I'm surprised ARKS (or "ARKZ") were the bad guys of the story. Though with how it's written, it seems like the Hunters represent Pioneer 2's potentially corrupt government while ARKZ are more of revolutionists than terrorist... which to any opposed government those words mean same thing I suppose.
(I made up a FOnewm named "Solitaire", I've yet to pick a side for him. I hope fashion is still a thing in PSO given I don't like his default jester costume.)
‘You either die a hero or live long enough to see yourself become the villain…’ – Mark Carrigan