I'm not quite sure how practical it is, but if you're looking for inspiration then might I suggest Babylon 5 and Battlestar Galactica?
I think a problem I have with a lot of Sci-Fi series is the way they're franchised. You have story arcs, followed by fillers, followed by the season finalle which inevitably culminates in a cliff hangar ending to keep the viewer watching... and repeat!
What really grabbed me about the 'Stories' above is that they are just that: Stories.
All right! So they're presented in a series format, but the new version of Battlestar Galactica in particular caught my eye. If you don't know the general gist (and where have you been the last few decades?) the Human civilization was founded on the planet of Kobol under a pantheon of Gods which very much resemble those in our own Greek Mythology.
Though in time a great cataclysm befell the planet stemming from the Human's own destructive ignorance, and were forced to flee their home as it became awash in fire! From there they took to the stars, forming the 12 colonies, one named after each sign of the Zodiac to represent each God.
Years and years down the line the civilization flourished, technology leading the way and finally to the creation of true A.I. - The Cylons
Originally they were meant to make lives easier on the billions of humans in the colonies, and as research advanced newer and newer models were created, finally with true sentience! If very logical and calculating.
As the old chestnut goes, they revolted. Being computer experts in their own right, the Cylons developed methods for infiltrating any networked computer system and shutting it down, thus most current ships of the time were rendered defenceless nigh instantly. The Battlestars were developed as a means to counter the Cylon threat, huge Warships capable of carrying a full squadron of the highly maneuverable space fighter; the Viper MK.2. Not only that, (and this is from the new series, remember) laser technology is practically none existant. Instead, the Battlestars are capable of launching a huge flack and ballistic screen, along with nuclear tipped missiles.
And why weren't they shut down? Simply because they had a large crew and no networked computers to speak of, so most complex equations and data transfers had to be done manually.
In the 100 years of war that followed, a truce was finally brokered with the Cylons leaving the Star Systems to find a planet of their own. However, they never forgave the ones they regard as their 'parents'.
Fourty years down the line they stage a huge assault, and thanks to a new model of Cylon, one outwardly undetectable from humans and with the emotional difficulties that comes with (12 human models in total, along with countless copies of each type) they infiltrated the Human defence systems and shut them down totally. The colonies were left wide open to an apocalyptic nuclear assault!
On this very same day the Battlestar Galactica was undergoing its decommissioning ceremony into a relic museum of the 40 years war, complete with a full squadron of the old MK.2s. Initially, it alone is the only apparent survivor due to its immunity to the crippling computer virus, owing to its lack of upgrades unlike the modern Battlestars and Viper MK.7 figthers, all of which were left defenceless hulks of metal floating in space.
Or, the only survivor along with a fleet of civilian ships left floating in space when the attack started. Their only option is to run, their only shelter the fabled 13th colony of legend: Earth.
Phew! All right, with that back story out of the way... Yes, I know I've just really taken my time over that, but there's a reason!
This is a very grim universe, literally the possible extinction of the human race. They only have the supplies they started out with, limited ammunition reserves (but it will take quite a while to burn through, I should think...) water, food, medicine and everything else! The point being, they have to somehow elude their Cylon persuers, scavenge what little resources they can (Such as Asteroids for specific gaseous compounds that can be used as fuel, planets and meteorites for water, etc...)
Now is it just me, or can this be adapted to become the player's choice? Yes, I know it moves outside the lore of the series... but perhaps other Battlestars survived (As one did, but that's the only spoiler I'm going to type here) which constitute other players. Maybe they banded together, found habitable planets and decided to make a stand against the Cylons?
What I'm trying to say is, if you adapt this sort of story in to a game format, leaving the players free to decide what to do after the colonies are crippled (obviously waving aside breeding times and other such real life fluff). What would you do? Develop Anti-Rad research and wrestle control of your Colonies back? Move on and look for richer grounds?
I'm not saying its the definitive story, I'm just saying it could create a cracking campaign and there are definitely some elements that spring to mind which would work wonders in a deep Sci-Fi mod. And hell, what else would it be with an engine like Sins to work on?
