The Commanding Officer (CO) of a starship or installation has the ultimate responsibility for the safety and well-being of their crew, as well as the responsibility to ensure that the ship's mission is satisfactorily executed. The Commanding Officer usually holds the rank of Captain, but smaller ships may see a Commander filling this role.
Duties[]
The CO has no set duty shift and is always considered to be on call. On larger starships the CO usually has his own office, and this office is sometimes very close to the bridge, offering quick and easy access in emergency situations. The CO is also responsible for meting out punishment for crew members found guilty of breaking major regulations. The Commanding Officer is also traditionally the member of the crew who performs such duties as marrying crew members under his command and serving as the host at all official functions held aboard his ship.
The CO's immediate staff are the First Officer, the Second Officer (if one has been chosen), and the chiefs of the other departments (the Department Heads), which make up the Senior Staff.
A Commanding Officer may also refer to any supervising officer that is above a subordinate. Example: An ensign who is a leader of a security team would refer to his department head as his Commanding Officer.
If a ship or station's Commanding Officer has been incapacitated, killed, is missing, or is otherwise unavailable aboard the ship for an extended period, another officer may step in. This officer would be known as the "Acting Commanding Officer" or "Acting Captain" until either the assigned Commanding Officer returns to their duties or Starfleet Command assigns or confirms the replacement.
Traditions[]
Traditionally, Commanding Officers on a starship are referred to as "Captain" regardless of rank (a tradition dating back to the days of earth sailing vessels), though some CO's prefer to forego this tradition. The two exceptions to this tradition are a visiting officer who holds the rank of Captain and any Flag Officer. Visiting captains are often referred to as Commodore to avoid confusion, and Flag Officers are always referred to by their proper rank, or informally as Admiral.
This tradition applies for any officer serving as a commanding officer of a starship, even if the current Commanding Officer is not the permanent ship's CO. Two examples of this are when Commander Jadzia Dax was assigned to command the Defiant for a few weeks, and when Lieutenant Commander Worf was in temporary command. In both cases, officers on the Defiant referred to the current Commanding Officer as "Captain" despite the lack of a permanent assignment or the actual rank of Captain.