The single player portion of Star Trek Starfleet Command III features separate Klingon, Romulan and Federation campaigns. There is also an Instant Action mode, and Conquest -- a simulated multiplayer mode where players vie for control of the known universe in an ongoing sector-by-sector battle.

Multiplayer modes in Star Trek Starfleet Command III includes Skirmish mode where players can engage in combat as the Federation, Klingons, Borg or Romulans in free-for-all and team-based games. Additionally, Star Trek Starfleet Command III includes an enhanced version of the Dynaverse 3 multiplayer environment. This persistent online component features improved AI and a new system that allows players to join the same fleet, travel together across the galaxy and battle alongside one another in a bid to improve their ships and carve out territory in the name of their empire.