The campaign (to be exact 3 campaigns with 88 missions)with the greatest and most complex storyline was Freespace 2 - Revenge: Final Conflict. I think, this campaign is from 2004 or something. I played it in german but I just found a newer english version. It seems, it has some problems with other versions than retail. Nevertheless a great story and a lot of different, mysterious missions:
http://www.hard-light.net/forums/index.php?topic=38610.220Story (as far as I know it after 6 years

) :
A few years after the orignial Freespace II campaign:
1. campaign (Kind of a long tutorial): GTVA has developed a lot of new ships and weapons and plans to investigate (and if possible expel the shivans). Therefore a new Knossos-Portal is built. The Hammer of Light return and try to hinder the GTVA, from using the gate. A new civil war begins, but GTVA remains in control.
2. campaign (Action with the shivans): A strong strikegroup attacks a shivan world. 2 ships, the GTVA Marco Polo (colossus class

) and the GTVA Malovolence (deimos class) are accidently pulled into a big - long distance - knossos portal. These two ships are on there on in a distant region of space, filled with a lot of shivans. Both ships heavily damaged and without new supplies are forced to play hide and seek with the shivans. First signs of an mysterious, but mighty enemy of the shivans appear.
3. campaign (Revenge): New allys are found and GTVA Marco Polo and Malovolence will be upgraded. A way back to earth is discovered, but another big problem has been discovered. A big shivan strikeforce with lucifer and sathanas ships is on its way to earth. Earth can't defend it self, because of special circumstances. (Don't wanna tell everything

) So it depends on you and your ships to hunt down the shivans, and to ensure that future attacks from shivan forces are impossible.
I really think it is worth a try, if you have a few days of free time.

Also a must have mod for every fan from ST Voyager or Battlestar Galactica.