AdvanceStrat: It is awesome getting to see this game again after so long ( we still have the original disks but they don't work so well with xp/win7). There was one question about the game I never really understood though.
It's been a while since I played the mission, and i haven't gotten that far yet in this run, but late in the game...
*SPOILERS*
If you side with King instead of the alliance, you get an extra mission as a navy ship where you get a choice between either going after the hospital ship, or shooting down your wingman and joining the alliance. If you side with the alliance, the story moves on as usual. If you follow orders and destroy the ship, you get an ending cutscene where you're basically a pilot for a space garbage truck due to blowing up the ship.
*END SPOILERS*
Obviously blowing up a ship like that is something you file under the "not good" category, but I never understood why you were punished by the navy for following the orders they had specifically given you for that mission. What was the deal there?
I don't know the exact reasoning behind that ending to tell you the truth. However I could easily imagine that you might get scapegoated for destroying the hospital ship by King's administration if the truth got out. They'd be looking for someone to shoulder the blame, and as you were following orders you might get demoted rather than punished more severely.