Who are your enemies in this game? Well, besides rival clans, people who interpret your particular holy writ just a leetle beet deeferently and, well, any military patrol you come across (because even if they're quasi-military, they've probably got a better ship) you've got the special forces of the God Emperor, "Himself."
There's the Faith Healers, those strange surgeons who keep Him alive...it is rumoured by dark technology. Others say that He has taken on genetic manipulation and become alien to even Himself.
That's blasphemy, you know. And punishable...by death.
As previously described, there are also Inquisitors and the Missionaries His guard and His spies. There are also his troops, the Clergy.