The story focuses on Domasi Tawodi (also known as "Tommy"), a Cherokee garage mechanic and former U.S. Army soldier living on a Native American reservation in Oklahoma . At the beginning of the game, Tommy is in a bar owned by his girlfriend, Jen. Tommy is tired of living on the reservation, and constantly tries to push his heritage away, while at the same time trying to convince Jen to leave home, if only for a short while, to which she refuses steadfastly. After an unfortunate bar fight, the entire building is lifted up by a gravitational force into a green light above. Tommy, Jen, and Tommy's grandfather, Enisi, are transported skyward to the massive alien starship called the Sphere. After docking, all three, along with countless other captives, are dragged through the upper levels of the Sphere. Tommy is freed in an explosion set off by a stranger who, despite being cybernetic like most of the Sphere's denizens, appears to be working against it rather than for it.

Tommy witnesses Enisi's death in a brutal alien device. While trying to find Jen, he falls from a walkway and has a near-death experience toThe Land of The Ancientswhere he meets with his grandfather's spirit who bestows him with spiritual powers. After returning to the world of the living, Tommy gains the ability to spirit-walk, allowing him to separate from his body to pass through forcefields and operate consoles normally out of reach, as well as the aid of his spirit guide , the ghost of his childhood pet hawk , named Talon. Despite being entrusted by his ancestor's spirits with the mission to protect all of mankind from the sphere's invasion, Tommy cannot stop worrying about Jen, and he only cares about how to find and rescue her.