It has been twenty years since the invading aliens have been driven back through the jumpgate. On a planet close to the dormant gate, an alien artifact is found. When unknown aliens steal the artifact, privateer Captain Flint of the spaceship Cortez and his crew follow their ship through the jumpgate, which leaves them stranded in an unknown star system. To find their way back, they have to find the artifact and the aliens.

You take control of Flint. Aboard the Cortez, you can receive messages from your crew members, scan the planets in the system for possible mission sites and select suitable weapons and equipment for the next mission. Three different craft are available for the missions: a fighter, a hovercraft and a stationary turret used to give cover to your crew mates when they are on a mission.

After completed missions, the wreckage from destroyed aliens is analyzed and used to produce better weapons and equipment. The storyline will take you through six different systems, each with a variety of missions to complete. Live-action cut-scenes continue the story.