The player controls the ship either directly with the keyboard/gamepad or by giving orders to the helm on a map of the current sector or by marking planets or enemies in directly on the screen. Depending on how well a mission is completed, the player can earn command points with which they can buy up to 4 ships, which function like a squad.
During the campaign, the player controls over ships of the United Federation of Planets and fights against Klingons, Romulans and the Borg. In skirmish and multiplayer, all 4 races are playable.