Initially all the commanders were of the same alliance: Empire. At some point, generally in the first third of the game, commanders would rebel from the Empire by choosing one of three factions (Environmentalist, Militarist, or Scientist) they preferred. Each faction had certain advantages. Environmentalists developed their colonized worlds in Environmental level without any special actions taken. This gave them more rapid advancement of Tech level also. Scientists advanced Tech levels most rapidly without special actions taken, even on worlds with lower Environment level the Tech levels would still advance faster. Militarists had the advantage of more firepower from offensive weapons and stronger defenses to better protect planets. The Empire and the Rogue factions had no special abilities.
After joining the rebellion all Empire planets and ships were enemies as well as planets and ships of the two other factions not chosen. Ending movement on an enemy planet resulted in combat with that planet. If enemy ships were also at that planet a battle would first happen with the enemy ships present and then with the planet after the ship to ship battles were decided if all enemy ships were eliminated. If a planets defenses were destroyed, the planet would then be captured and added to that commander’s list of controlled planets.
Later in the game, a commander could also elect to become “Rogue” which meant all other players would be enemy regardless of which faction they belonged to. This was a useful ability to enable the taking of planets from another player of the same faction.