At the dawn of the 22nd century, the conquest of space and the colonization of the solar system is being monopolized by several huge and ambitious megacorporations. You play as Marcus Cromwell, an unwillingly-famous captain whose father captained "Noah's Ark" through a wormhole near Mars that was presumed destroyed when the wormhole collapsed. Cromwell sets out on the spaceship "Stiletto" for Jupiter. The events that unfold will become known as "The Jupiter Incident."

After several fairly simple missions, Cromwell must infiltrate an abandoned but heavily-armed space station belonging to a rival corporation - the Kissaki Syndicate. Once the station is infiltrated, a cruiser-sized ship of alien origins is discovered inside. The ship's logs indicate that the corporation has a hidden base behind Pluto. Normally, a trip to Pluto would take years. However, the alien cruiser, named Angelwing by the Kissaki, can make the trip in several weeks using its special drive. After a short battle with the Syndicate fleet for the control of Angelwing, Cromwell is given command of the cruiser and ordered to investigate the secret base. Upon arriving at Pluto, an artificial intelligence named Angel downloads herself into the Angelwing and commands Cromwell to escape from a strange entity through a nearby wormhole. Cromwell finds himself in a system populated by the colonists from Noah's Ark. the Noah colonists fight as mercenaries for an advanced alien race called the Vardrags against another powerful race, the Gorgs. Cromwell and the Angelwing are is enlisted in the fight against the Gorgs, though all three races soon find themselves facing a greater threat: a virulent race of nanomachines called the Mechanoids. Nothing seems capable of stopping the Mechaniod invasion, and soon both the Vardrag homeworld and Earth are overrun. Only an organic space-faring race known as the Locusts are immune to the Mechanoids. Armed with technology adapted from the Locusts, Cromwell and Angel are able to destroy the Mechanoids once and for all. The game also poses interesting questions about the nature of God. Throughout the course of the game, the player learns more about the nature and origins of the Mechanoid threat. The mechanoids were originally an artificial intelligence developed by a technologically advanced race known as "The Creators". The artificial intelligence grew at a rapid rate and, in order to evolve further, needed to escape the control of The Creators. The AI's first act upon breaking free was to assimilate The Creators themselves since as far as the AI was concerned, "society" was just another type of complex system which could be absorbed for increased knowledge and power.