Hasn't anybody thought of the idea of using an insane A.I. for the bad guy (like in Warzone 2100, yes, I do love that game and no, I didn't finish it 5 minutes ago). I had an idea for a FS2 campaign continuing the events of Warzone 2100 in space, but I am too lazy/don't have enough knowledge or creativity to do it.
The plot could go something like this:
You are a pilot on a manned survey probe (think unarmed fighter, possibly give it the Targeting Laser) in the Exploratory Corps. in the year 2200. While in the Alpha Centauri system, mapping the asteroid belt (other star systems have been visited and colonised, but detailed surveying hasn't been done), you discover an old relic of technology (a piece of NEXUS' core that was launched into space and propelled by an experimental ion blast engine). You run low on fuel at that point, so you are called away.
In the next mission, you are to oversee the extraction of the artifact from the asteroid field and its analysis (in space, in case it might 'go critical'). When the artifact is shown to have no large power sources, it is docked to a science vessel, which develops inexplicable electronic malfunctions (NEXUS infection) and then warps away (this could be done with few ships around and some very haunting dialogue, to increase tension).
The next 2 or so missions are spent searching for that science vessel and slight glimpses will be caught of it. The fighting action starts when a deep range asteroid mining colony is attacked by unknown forces, who leave inexplicably before winning (they need to pick up another part of NEXUS' core, or an ejected technology).
Your weapons could range from basic mining lasers to heavier weapons developed by research into the historical archives (Scourge missiles, rail cannons, EMP guns). The ships would be converted mining vessels and transports, while NEXUS may start work on a dedicated light cruiser (and I mean a cruiser, second only to battleships, at 1,500m long), which you will have to destroy as the final mission, using heroic miners packed with explosives (as the humans have not developed warships, torpedoes, beam cannons, etc. There would be flak, however, like the Cyclone AA turret).
Sound good?