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The Command Department is mainly responsible for the ship and it's crew, and those within the department are responsible for commanding the vessle and representing the interests of Starfleet.
Commanding Officer - Ultimately responsible for the ship and the crew, the commanding officer is the most senior officer aboard the vessle. S/he is responsible for carrying out the orders of Starfleet, and for representing both Starfleet and the Federation.
Executive Officer - The liason between captain and crew, the Executive Officer acts as a disiplinarian, personel manager, advisor to the captain, and much more. S/he is also one of the only two officers, the other is the Chief Medical Officer, capable for removing the Commanding Officer from duty.
Second Officer - Acts as the executive officer in the event that the CO or the XO is incapacitated. The second officer usually holds another postion aboard the ship.
Chief of the Boat - The senior most chief petty officer aboard the vessle, in addition to his or her duties as a member of the crew, the chief of the boat also serves as a liason between command staff and enlisted crewmen, acts as a disiplinarian for enlisted crewmen, and overal is responsible for all enlisted crewmen aboard the vessle.
Responsible for the navagation and flight control of the vessle and it's auxilary craft, the Flight Control department includes trained pilots in both flight of starship and auxilary craft piloting. Note that the Flight Control department doesn't include Fighter Pilots.
Chief Flight Control Officer - A department head, and a member of the bridge crew, the Conn, as s/he is called, is responsible for navigating and piloting the ship during most major encounters.
Flight Control Officer - A Flight Control Officer is required on the bridge at all times; as such, they act as a helmsman and navigator when the Chief Flight Control Officer is not at the helm. They also assist their department head by plotting courses and supervising the computers piloting.
Shuttle/Runabout Pilot - Responsible for piloting various auxilary craft, (excluding fighter craft), these pilots are responsible for transporting their passengers safely to and from locations not reachable by transporters.