"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 back 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 where 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 can't stop worrying about Jen, and he only cares about how to find and rescue her.
[edit] The Sphere
Artwork depicting The Sphere as viewed from space.

The Sphere is an organic alien ship. It has a small, concentrated star at its core, which is used to support itself and all life inside it. The origin of the Sphere is unclear, but its main goal is to maintain itself. It travels the galaxy searching for various alien races to maintain it. It also uses these races as food to provide much needed extra energy to sustain the Sphere and its star. The Sphere is fused with cybernetic enhancements, and has the power to manipulate gravity inside of itself and alter space (as demonstrated in the maze puzzle and in the numerous small storage boxes that, when entered, lead to entire rooms). Various walkways allow the occupants to walk on surfaces otherwise designated as walls and ceilings. Switches that change the direction of gravity, effectively changing the orientation of anyone in the area, are present in some locations, causing floors, walls, and ceilings to change their roles depending on the switch used. The Sphere also has the ability to produce portals to other sections at will. These portals allow occupants to move much faster around the Sphere and fulfill their duties more efficiently.

The Sphere houses many different alien races that were taken by the Sphere from other worlds. Most of them are cybernetically enhanced, much like the Strogg of the Quake series, and they have a language of their own, unreadable until Tommy obtains Talon and their language is translated to English.

It is implied along the game that the Sphere races plant the seed of life in certain worlds that they see have the potential to sustain such life. Once the seed is planted, they let evolution run its course while they go to other worlds. However, once the planet is brimming with life, be it intelligent or not, they come back to "reap" all resources, both organic and material from the planet.

Multiple species may be consumed as more energy for the Sphere. The only group of beings aboard the Sphere who live relatively freely are a small band of humans who call themselves the Hidden. The members of the Hidden, individually known as "Hiders", are slightly enhanced with cybernetics, but nowhere near the extent of the other beings on the Sphere, and have not lost their individuality. Led by a seemingly young woman named Elhuit, the Hidden strive to ultimately destroy the Sphere, though what they want most is to return to Earth, where they were taken from many years ago.

The Sphere is controlled by a superior being called "The Mother" who communicates telepathically with Tommy throughout the game. She reveals to Tommy that she was once human. She too once fought against the previous "Mother" of the Sphere and after defeating it, she took its place. At the end, after a very turbulent fight, Mother is defeated and, in her death throes, begs Tommy to take over her job, lest the entire Sphere die. As she dies, a burst of light engulfs Tommy and when vision is restored, Tommy finds himself inside the Mother's den with reams of data overwhelming him, making him numb with power. His grandfather, Enisi, contacts him from the spirit realm and tells him that such power is only an illusion, as the price is greater than what he has gained, and that he needs to look in his heart and make the right decision. Tommy heeds his grandfather's words and drives the Sphere straight into the Sun, and ends up in the land of the ancients to see Enisi and Jen once more. Knowing that when it is his time he will see them both again, Tommy goes back to Earth.

Six months later, Tommy finds himself in a rebuilt Roadhouse, apparently not yet open to the public. The official story is that people, buildings and objects vanished because of an unknown, unexplained natural phenomenon. He turns around and sees Elhuit. She and the surviving Hiders had escaped through their own portal machine just before Tommy plunged the Sphere into the sun. She tells him that while people on Earth do not know of the great deed he has done, there are those "elsewhere" who have taken notice and want to meet him. Elhuit opens up a portal and Tommy walks through it. The words "Prey will continue..." appear."