Appointed only by the Admiralty, this character has the responsibility of commanding the entire Starbase. All other characters are under his/her command. The character for the commander should have a professioanl personality, garner respect, and communicate with all characters. He/she should be able to work with the crew to accomplish dangerous or complicated missions.

In addition, the person who writes for and plays the commander is responsible for selecting new missions for the SIM, guiding the story line, overseeing and resolving player conflicts, recruiting new members, and maintaining the list server and website for the Starbase. He/she is the final authority for any decision for the sim. The player who takes a CO position should be able to manage groups of writers and give advice and encouragement to all players.

This character usually plays on the Command Center, but can be moved all over the facility and on some selected away missions. This person is one of the main characters in the SIM and is always heavily featured in all missions. The CO is the most time consuming position due to all the intra-story duties required of the "captain".

Examples from Star Trek are Capt. James T. Kirk, Capt. Picard, Capt. Janeway, and Capt. Jonathan Archer, Capt. Benjamin Sisko.