Most of the game is set on an alien world light years from Earth, but it begins 120 years in the future on Earth with a young graduate of West Point, Charlie Campbell as he prepares to join the crew of Morning Star Research Vessel (MSRV) Joplin to investigate an intelligent signal they received from Saturn's moon, Titan. The crew encounters a powerful artifact of obvious alien design, and after Charlie activates it, the rest of the game follows him as he travels back-and-forth from the Joplin to an alien planet whose mysteries he begins to discover.

As Charlie continues his journey, he learns about his mission, the intra-governmental agreement that sent him out to the outer reaches of the Solar System, and the conflict that he encounters on the alien world. With the help of his crew, he also starts to figure out how to undo the awful events of the early portion of the game by harnessing the changes that he begins to undergo.