I read about the plot description on the main page and noticed, there wasn't much of that actually in the game! So I brought it upon myself to come up with a few ideas of how it may work.
How I think it may work, is you go from planet to planet, helping out the civilians or doing another type of goal. When you complete a planet's goal, you can still return there or stay if you wanted, but you also unlock the next planet in the system. Complete all the planets in a given system to unlock the next one. You can always return to previous planets/systems if you wanted and your stuff will still remain, so if you liked a certain area, you can stay.
These are all the ideas I have so far, but feel free to reply to this topic or comment on the document if you had any ideas, suggestions, or constructive criticism!