When doing long term space trucker campaigns there's a lot that could happen without involving xenomorphs, I found out that for my group it works better if there isn't a general plot guiding it all, at least in the beginning, but rather to focus on specific, shorter adventures, and then, later, if they're still alive, just develop some plot point that may have interest and evolve it into a larger story. So I just prepare different plot hooks and let them decide, as a crew, what will be the next job. Then, depending on how things develop, just go one way or another.
At the risk of getting yelled at for "crossing the streams":
There is an RPG game like this which has been kicking around for ... about 40 years  which has running jokes about it being used as a basis for ALIEN games since the early 80s .
It has a wealth of "space trucker" friendly material for it that is not at all troublesome to adapt to an ALIEN universe.
Recent editions and an open spin-off heavily feature supplements written by one of the contributors to the ALIEN RPG itself  
 Yes, I mean Traveller - patron encounters, spaceport encounters, and much more can be mined for inspiration.
 JTAS 4 contained stats for "Reticulan Parasites" which led to people asking "we're really playing Traveller right, not Alien?" because GMs would liberally sprinkle said parasites into games without warning.
 Zozer Games' CREW EXPENDABLE supplement for HOSTILE can flesh out and supplement an ALIEN RPG game "Space Truckers" game quite nicely.
 Zozer Games' SOLO supplement for Traveller can be used to solo play a Space Trucker style game as a mine-able testing ground for a "Space Truckers" campaign with friends.
We live, as we dream -- alone. ~ Joseph Conrad