Ok, cool idea here.
The player never gets arrested. He didn't actually break any laws.
But he gets kicked out of Star Control, and loses his rank. The humans don't trust a captain who would sell crew. You keep your ship and fleet because you built them technically as a Pkunk captain. So alliance bases no longer do business with you, and you are unpopular with many of them.
This makes it open, and the player can clear the accusations at any time.
You can keep the moral dilemma by having certain things that make the game easier if you steal them from the alliance, although it will make other parts of the game harder because you won't have full cooperation later. Whether you steal also affects the ending, and some other moral dilemmas in the game would be the Chmmr and the AI controlled ships.
Actually that's not a problem. It is indeed possible and even likely that the Ur-quan original HW was somewhere in the area of SC2's starmap since the Taalo are the ones who met them, however it doesn't have to be that way since the milieu did span over most of the galaxy. At any case the Ur-quans did not start their paths in their HW - they did it in the area of the Maul-num HW, where the first doctrinal war begun.
Which means that the Maul-num HW is more or less in the opposite side of the galaxy then ours.
Good point.
I like the last idea. We don't really have to answer who warned the Niko or why. The player will learn that it happened around 2,400 years ago, which is 100 years after the Gzerllion left the Ger, but that's the only thing he'll find.
Whoever saved the Niko did it while they were still fairly primitive, and instructed them to "spread the word, warn others and prepare themselves for the coming of the evil Kohr-ah."
Over the years the Niko developed into the theocracy they are now, with corrupted and power hungry "Church of Ssssirpa" as their leaders.
Their belief is now that anyone who follows the Church of Ssssirpa is protected from all harm, and that everyone must be converted into followers.
The player coming and claiming that the Kohr-ah are defeated will only cause them trouble and convince them that removing him from the picture is essential.
Yes, although while he is a threat they want to discredit and get out of there, he also gave the Niko credibility in the point of view of other new arm races, which makes their joining when the Mrmrnmhrm show up more logical.
As for Ssssirpa actually being the Gerzillion (who warned races in the area), that's actually a very cool idea. Maybe he gave them technology for space travel, proving his divine nature and greatly influencing Niko cultural development. Though, as I saw it, the church of Ssssirpa was not the only religion on their planet, and the Niko had many competing religions, explaining the drive to convert by force and make church leaders powerful. Maybe the Gerzillion happened to match Ssssirpa most out of all the Niko religious concepts, and that's how the church got power, or the church of Ssssirpa was started immediately when the Gerzillion showed up. But if Ssssirpa actually exists, that means there's no secret the Niko leaders are guarding, and doing the Mrmrnmhrm plot suggests doubt in the existence of Ssssirpa. And how would they explain the similarity of the Gerzillion legend to Ssssirpa (unless both became so exaggerated in legend that the 2 were not that similar)?
Of course, I'm still partial to the idea that the prophet of Ssssirpa got drunk and came up with doomsday (which he just happened to be right about) in a stupor, and that's the big secret that you keep trying to learn about the Niko origin, because I have an odd sense of humor. The idea of a doomsday cult with questionable origins happening to be right by luck amuses me. Maybe both ideas could work if the prophet made the prediction before the Gerzillion showed up, confirming it and becoming Ssssirpa in their legends.