You'll need some group of fanatics somewhere in the galaxy. What exactly they're fanatical about is kinda vague and unclear. But they want to recruit the player to do courier missions and such. Then, as the side string progresses, you start getting suspicious and think you're working for some bad guys. You think you may be delievering terrorist plans, bomb scematics, etc.
But then, right when you would be expected to betray them to the police, they come clean, and you find that they're just a peaceful resistance group attemping to free an enslaved/badly treated people. So at the end, you help free these people, they get they're own little planet somewhere, and you get booku mega discounts there. Plus, the BBS there will occasionally have extra, well paying missions. Like routing out remaining strongholds of their previous oppressors, or opening talks with existing governments, or shipping in supplies their new world is short on. Make this route give you a universal gov't rating boost if possible, not a lot, but enough to make you respected throughout the galaxy.
Or, you can betray them. But then you find out you screwed up and blabbed to the government/organization that is doing the above mentioned repression. The group is destroyed but the repressed people manage to escape in the chaos of the fighting, they still get their planet, but instead you can't land there and they're ships will attack you on sight.
Or, you can just quit working for them. In which case the people are freed, get their planet, but don't really care about you either way. You can land on their planet, but get no discounts or random extra missions.
Not sure if this can fit in at all with your galaxy, but I think it'd be a neat side string to include.
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