Commanding officer

A commanding officer (or CO) is a term used to describe one's rank in relation to others within the same environment.

Military units
One meaning of commanding officer is the highest-ranking officer and commander of a unit. On starships, the CO usually have the rank of captain, though sometimes a commodore or fleet captain may have also held this position. On starbases, the CO was sometimes referred to as "portmaster" and was usually a flag officer. Some bases, however, were commanded by captains or commanders. (Star Trek: Deep Space Nine seasons 1-3; )

It was also possible for lower ranks to be the commanding officer aboard a starship, such as the case with Lieutenant Commander Tom Markel aboard the USS Ariel. Other examples include Starfleet Command temporarily assigning a number of officers to command vessels that blockaded the Romulan support of the House of Duras in 2368. Benjamin Sisko commanded the Defiant as a commander for nearly a year before he was promoted to captain. Lieutenant Commander Piersall commanded the USS Prometheus (NCC-71201) in 2370. Major Kira Nerys and Lieutenant Commanders Jadzia Dax and Worf commanded the USS Defiant (2370) on a number of occasions. In 2373, Major Kira commanded the Defiant to destroy a Klingon minefield near the Bajoran system. Commander Worf assisted Captain Sisko in 2372 by bringing the Defiant to Earth to help quash Admiral Leyton's attempted coup d'état. Later, Worf helped his former commanding officer, Captain Jean-Luc Picard, in the Battle of Sector 001. Commander Dax commanded the Defiant in 2374 while operating out of Starbase 375. Her mission was to destroy a Dominion sensor array hidden in the Argolis Cluster. 

On starships, it was general practice to address the commanding officer as "captain," regardless of their actual rank or position. 

In general, commanding officers were dressed in the colors of the command division, but there were some exceptions in Starfleet uniform usage.

In rare occasions, the commanding officer needed not be a ranking officer, especially in dire circumstances. 

Dukat once claimed it was Cardassian tradition for the commanding officer to entertain his guests. 

Chain of command
The term "commanding officer" could also be used to refer to the officer whom one directly reported to in the chain of command or in a department. Occasionally, it simply identified an officer of higher rank in comparison to another, or the officer with the most experience if more than one officer held the highest rank at the time, although this was usually referred to as a ranking officer.

Leonard McCoy once pointed out to Spock that both of them answered to the same commanding officer, in which case he was referring to James T. Kirk. 

Lieutenant Commander Geordi La Forge once referred to himself as the commanding officer of Lieutenant Reginald Barclay. 

Commander William T. Riker was adamant about following the orders of one's commanding officer when confronting his transporter duplicate Thomas Riker. 

The Romulan defector "Setal" admitted to William Riker that his commanding officer was Admiral Alidar Jarok. 

Worf acknowledged the fact that Riker was his commanding officer before the latter agreed to the former joining him on an "unannounced visit" to the J'naii planet. 

Riker again brought up the issue of one's commanding officer when he, under threats by Arctus Baran, demanded that Data withdraw the USS Enterprise (NCC-1701) from their attempt to stop Baran's mercenary ship.