These include retreat, stop and shoot and pursue. There is also a pursuit instruction available for pursuing enemy units spotted at the start of the turn. These special orders allow some greater intelligence for your units, whilst forsaking some degree of control by the player. These settings will also depend on the unit type. For example, you will normally want your medic to retreat when he spots an enemy.
Players choose between three factions - marines, droids and aliens.
The first player chooses one of the three factions, and the second player must choose one of the remaining two. Each faction has five distinct unit types, some with special abilities. For example, the aliens have a 'queen' breeder unit that can lay eggs depending on consumption of enemy corpses. The droids have a scanner unit for detecting organic brainwaves through solid walls. The marines have medic units for battlefield surgery, etc. etc.