Commanding officer A commanding officer ( abbreviated CO , or also simply commander ) was a term used to describe one ' s hierarchical position in relation to others within the same environment . Military units . One meaning of commanding officer was the highest - ranking officer and commander of a unit . On starship s , the CO usually held the rank of captain , though sometimes a commodore or fleet captain may have also held this position . On starbase s , the CO was sometimes referred to as " portmaster " and was usually a flag officer . ( ) Some bases , however , were commanded by commodores , captains or commander s . ( seasons 1 - 3 ; ; ) Commodore Matt Decker , mournful of the loss of his ship and crew , explained his rational for his suicide run at the " planet killer " , stating , " " The commander is responsible for the lives of his crew . . . and for their deaths . Well . . . I should have died with mine . " " Kirk , in turn pleaded " " You can ' t throw your life away like this . Matt , you ' re a starship commander . That makes you a valuable commodity . We need you . . . your experience , your judgment . Matt ! We ' re stronger with you than without you ! " " ( ) 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 . ( ) Other examples included Starfleet Command temporarily assigning a number of officers to command vessels that blockade d the Romulan support of the House of Duras in 2368 , including Lt . Cmdr . Data aboard the . ( ) Lieutenant Commander Piersall commanded the in 2370 . ( ) Benjamin Sisko commanded the " Defiant " as a commander for nearly a year before he was promoted to captain . Major Kira Nerys and Lieutenant Commanders Jadzia Dax and Worf commanded the 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 some cases the term " commander " was the chosen title . 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 . ( ) The Takret Militia soldier s also refer to their superiors as commanding officer . ( ) As did the Kelvan and the Kalandan people . ( 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 . ( ) Kirk , who greatly lamented the loss of three of security men on Gamma Trianguli VI , had his self - recriminations reassured by Spock , who explained that " " No one has ever stated that Starfleet duty was particularly safe . You ' ve followed the correct and logical course , done everything a commander could do . " " ( ) 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 from their attempt to stop Baran ' s mercenary ship . ( )