Chain of command The chain of command was a rank ing system used by militaries and other organized groups . It represented the line of authority down which orders are passed from one officer to another , and also the line down which passed command of a particular vessel or installation . Aboard a starship , or most starbase s the chain of command began with the assigned commanding officer , usually an officer of the rank of captain , or in some cases commander . If the commanding officer , for any reason , was unavailable to command his or her post then those responsibilities passed down the " chain " to the first officer , then the second officer , etc . Between the launch of and the late 23rd century , the position of first officer , or executive officer ( abbreviated as XO ) was filled by the highest ranking officer assigned to the ship aside from the captain . The position was not a separate assignment as it would later become . The designated first officer would perform their normal duties until it became necessary for them to take command . This had changed by the late 24th century , when the XO ' s position had become a completely separate position in a starship ' s crew held by an officer of commander or lieutenant commander rank grade who held no other position aboard the vessel . After the executive officer , command responsibilities passed down the chain from officer to officer as necessary in accordance with each officer ' s rank . And it was common practice for a commanding officer to designate a second officer to take command if both the captain and first officer were unavailable or unable to perform their duties . Aboard the , Lt . Commander Data served as second officer . This aspect of the command chain functioned similarly aboard a starbase , or space station , as well as in a planetary installation . More broadly , the chain of command could refer to Starfleet , in general , with the chain beginning with the admiralty . And the Federation Council , and / or the President of the Federation could be considered to be at the ultimate top of the chain . When Captain Jonathan Archer reverse - imprinted on a group of Xindi - Insectoid s , his increasingly unusual actions led some of his fellow officers to openly question or defy his orders . He relieved those officers and stated Major J . Hayes that he needed officers who could respect the chain of command and follow orders . ( ) Mutiny is an inherent violation of the chain of command , something that was not lost on Captain Philippa Georgiou when she ordered Commander Michael Burnham arrested for incapacitating her and attempting to order a preemptive strike on the " Sarcophagus " . ( ) When Spock inquired to Dr . McCoy if he had noticed Captain Kirk acting strangely lately , McCoy replied , " " the man on top walks a lonely street . The chain of command is often a noose . " " In response to McCoy ' s words , Spock told him to " " spare me your philosophical metaphors . " " Spock then pointed out Kirk ' s transfer of Kevin Riley to engineering , and McCoy explained that " " he ' s the Captain , he can transfer whoever he pleases , " " adding " " you can look that up in a hundred volumes of space regulations somewhere . " " ( ) Benjamin Sisko learned many things from Captain Leyton aboard the , including that " a good officer has to respect the chain of command . " Leyton believed that without it " Starfleet would cease to function and we wouldn ' t stand a chance against our enemies . " ( ) Starfleet Command thought Constable Odo ' s respect for the chain of command was " minimal . " ( )