

Lyran Star Empire (Iron Fang, Red Claw, & Mountain Watchers) – The internal political squabbles fo the various Lyran clans must be put on hold when it is discovered that an old enemy is attempting to conquer from within. Romulan Star Empire (Tai Praiex, Tal Shiar) – The outbreak of a plague sees the Romulan Empire doing what is necessary to combat it, before political machinations by the leader of the Tal Shiar throw the future of the Empire into question.

Klingon Empire (Black Fleet) – After confirming that the Organians have departed for parts unknown, the Klingon Empire attempts to take advantage of heightened galactic tensions, before discovering that an ancient enemy has returned from beyond the grave with vengeance in mind. United Federation of Planets (Starfleet Special Task Force) – After it is confirmed that the Organians have departed their planet, Starfleet beings to develop new weapons systems, before discovering that forces from the Terran Empire have somehow crossed over from the mirror universe and are attempting to take over the Federation.

These missions are triggered by joining the elite organization(s) of a various faction. While the basic campaigns are meant to emulate the 'General War' period of the Star Fleet Battles timeline, the main storyline of Starfleet Command spans several unique faction-based missions, focusing on the disappearance of the Organians. Starfleet Command is an open world game a player's actions during a mission will affect the game world (i.e, if the player succeeds, their chosen faction also succeeds).
