Command Department
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The Command Department includes both the senior-most officers of the unit, as well as administrative support personnel. On the largest units (such as starbases) there can be dozens of people in the command department, while on smaller units it may just be the senior officers and a yeoman or two. Smaller units also often combine command-related departments such as Strategic Operations, Intelligence or Diplomacy, if officers in those specialties are present.
Duties
The Command Department has some of the most complex duties of any department in any unit, with wide-ranging responsibility for the safety of their command, being the final word on navigation, engineering readiness, security, crew discipline, and even diplomatic decisions that might have repercussions for the entire Federation. The buck stops with the Command Department and the captain, on every non-medical issue.
- Carry out the orders of Starfleet, and represent the United Federation of Planets.
- Ensure all departments are properly staffed with qualified personnel, and supervise all departments in the performance of their duties.
- Ensure the safe navigation and readiness of their unit.
- Serve as the ultimate disciplinary authority within their unit, up to and including recommending courts-martial when necessary.
Standard Command Positions
Commanding Officer

Starships are rarely commanded directly by flag officers more senior than commodores. For the flagships of more senior officers, it is very common for the ship to have its own captain, who handles the day-to-day running of the ship. Historically, this officer would be called a flag captain, but the use of this term varies based on officers' preferences. Typically, a flag captain is relatively junior in seniority, given that they are closely supervised by their flag officer.
The captain of a starship has significant powers deriving from the difficulty of real-time contact with Starfleet, including the power to negotiate treaties and trade agreements when out of touch with Command. They also have authority over lesser vessels (such as tankers, freighters, passenger ships, etc.) during emergency situations. Similarly, commanding officers of starbases are often the senior-most officer in their sector with corresponding authority over starships in that sector.
Executive Officer / First Officer

First officers have important responsibilities in several emergency and contingency protocols, including needing to concur with the commanding officer's decision to self-destruct the ship or station in most circumstances, and needing to concur with the opinion of both the ship's counselor and the chief medical officer in circumstances where the commanding officer must be relieved of duty.
On larger commands, this role is most often separate, but on smaller vessels (and historically in Starfleet) it is often a dual-role for one of the department heads. In this case, they wear the color of the department that they also head.
Second Officer

The very largest commands such as major starbases might have a dedicated second officer within the command department, but this is uncommon aboard the average station or starship.
Yeoman

Additional Command Positions
Records Officer

Officer of the Watch
It is standard practice to have bridge-qualified department heads take the conn (i.e. command the bridge or operations center) when the captain, first officer, or second officer are otherwise occupied. Some starships have additional command department personnel who routinely stand watch on the bridge; most often this is a dedicated night-shift officer of the watch, but the largest ships might have up to six or seven officers between the rank of lieutenant junior grade and commander who are assigned to specific watches. This is more common aboard stations.
Command Master Chief
The Command Master Chief is the senior-most enlisted member of a unit, and might have additional responsibilities related to meeting the needs of the unit's enlisted population. This responsibility overlaps with the executive officer's responsibility for crew readiness and the counselor's responsibility to help address crew needs. While not all units have someone in this role, its value is in being able to provide the perspective of someone who's successfully navigated an enlisted career path to help train other enlisted personnel. As suggested by the name, this is generally a master chief petty officer, but lower enlisted grades could hold a modified title (Command Senior Chief, Command Chief, etc.) if necessary.
The Command Department In-Play
- This is both the most important and the smallest major department aboard any ship or base.
- Only very large ships or stations would have many people in this department beyond the CO and XO.
- Officers of the Watch have likely been seen on screen (for example the officer in command of the Prometheus on DS9 held the rank of either lieutenant junior grade or lieutenant commander (depending on if we accept the costume or how he was addressed) and may have been an Officer of the Watch rather than the ship's captain) but the idea here is 'extra' command-division junior officers who are specifically there to take over the bridge when necessary, especially on larger ships and starbases.