I was thinking about ST:Reborn and found some ideas for the FS port team too think about that might help them with it.
A thought came to me that the GTI could have reaserching the Nebulas in the systems around Ross128 to see if there were any Shivans left after the Lucifers loss.
Heres how it would go:
They found they were there and started to reaserch shivan tech by captureing Shivan ships. They were working under a feamale commander named Rigoss Monta, she would be the so called leader of the op. You would do some missions under her leadership and the big target would be a mission where you would have to capture a Shivan distroyer but it is a bust, and your left for dead when the mission is scrubed for no reason that you or your wing mates could find.
Then they suddenly transfer you to a new unit and you have to find a way out of the GTI and back to the GTA command in a covert ops escape mission like the one in FS2 only a little harder with a cruiser, and some transports you got to blow up.