When an avatar holds a troop berth on board a spacecraft it has authority over the turrets of the ship. They are responsible for the defense of their vessel, such as in case it is being boarded by intruders.
Unlike NPCs, an avatar is not required to hold a troop breath in order man turrets. So troop berths are normally only given to avatars if there are no other berths available or they can't be trusted with a command position onboard the spacecraft.
Troops spawn with the best armor and handheld weapon available from their spawning city. Weapon preference is as follows:
Military buildings with soldier guard posts will spawn soldiers, which will then defend their area.
Troops will operate the turrets or stand guard at specific locations on their stationed spacecraft. Troops that exceed the turret or guard duties will stay in the barracks and wait for vacancy, they will however also chase down intruders.
Ordering a troop to garrison will cause the troop desert if ordered to garrison any location other than a base. When garrisoning a base, the troop will join the base's soldier population.