GOOD, A
Join the good guys - kill the corrupt president - win the war
GOOD, B
Join the president for loyalty reasons - get orders to destroy hospital transport - refuse to kill them, and instead turn on your triggerhappy wingman - rejoin the good guys, and kill the corrupt president to end the war.
What I loved about this one, was that there was no
direct hint or quest marker that told it was possible to turn sides! Only a very subtle comment from your character, which could have been taken two ways.
BAD
Join the president for loyalty reasons - get orders to destroy hospital transport - comply with killing them - get kicked out of the navy once the good guys won the war - regain command of a new ship after the war (a literal garbage transport ship)
NEUTRAL ENDING
Skip the entire 'mysterious ships' plot - attack and destroy a large Indie base - big victory for the Commonwealth, but the war still continued.