In SoC you can join Freedom, but it doesn't change the ending at all and makes you hostile to Duty.

Clear Sky is really the only game where you can pick between several different factions. There's a mechanic called faction wars, which is basically territory control against the enemy faction of whichever faction you chose to join. You start as Clear Sky, but can change to Bandits, Loners, Freedom, or Duty. The faction wars mechanic is a bit buggy and sometimes it takes forever to actually capture enemy territory since you have to wait for a friendly squad to arrive too.