Gameplay consists of maneuvering one's ship to approach enemy ships and assault them in the areas where various systems and ship's shields are vulnerable. It also consists of achieving various other objectives specified in mission assignment, which are provided at the beginning of each scenario. This can include interacting with various ships, aliens, planetary bodies, and other objects in space, depending on the specific assignment.
Though the game has no central story-mode campaign, players may play as any race, each one having at least one elite organization that, when joined, will trigger special missions that tell various stories. Though having unique stories, each race's special missions all contribute expository information on the fate of a race known as the Organians, and the effect that their departure from known space has since caused.