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 huge burst of light engulfs Tommy and when vision is restored, the player sees Tommy inside the Mother's den, complete with swarms of data overwhelming him. Once the process is complete, we find that Tommy is basically 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. No one on Earth knows that Tommy is a planetary saviour. He turns around and sees Elhuit, who he thought had died when the Mother located and attacked the Hidden's base of operations, suddenly standing across the bar. 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, which looks different from the others in the game, and Tommy walks through it. The player sees a mixture of light as the view warps towards the final destination and the screen goes black as the words "Prey will continue..." appear.