hmm InoCo has storyline?
I've done NESF, then MSF, then InoCo (after SAM "arrested" Dickens I had to go to Alex storyline - the one with Templars), and I've just finished USS storyline (which resulted into Triada)
so basically there are just few storylines, but based on your decisions, each ending is slightly different (and nothing can stop army of symbionts from attacking in the future it seems..). I'd like to know what lines remains, so I'll probably run a new game as soon as I fix those errors
Spoiler alert!
Triada has pretty hard ending, going into SAM's nest at precursor portal ALONE.. My Liger with 8x Vindicator turret (best rapid) and 2x Basilica turret (best plasma), 26k shields and 50% laser deflection hardly made it, with half fighters destroyed - though Living Legend animation was cool 
MSF has nice ending too, if you stay with Viper and won't join Trump
I really can't wait for datadisc (I hope that we'll get more free time to annihilate pirates, explore map and so on, random missions would be nice too