After Zia (Patrick Fugit) takes his own life, he finds himself in an afterlife limbo much the same as life, but slightly worse. The color is dim, there are no stars, and no one can smile. This strange realm is populated by people who have died by suicide, such as Eugene (Shea Whigham), a Russian musician who lives with his mother, father, and brother – all suicide victims. Together they waste most of their afterlives in bars, until Zia learns from a friend, Brian, that his ex-girlfriend, Desiree (Leslie Bibb), took her own life shortly after Zia’s death. He and Eugene take to the road to find her in Eugene’s rundown car. Early on, it is revealed that Eugene’s car has two idiosyncrasies, a black hole underneath the passenger seat where items that are dropped disappear forever, and broken headlights that cannot be fixed by even the most adept mechanics. On their trip, they pick up hitchhiker, Mikal, who insists she has arrived by mistake, and is seeking the “people in charge” (a.k.a. the PIC) in order to be sent back.
After a few adventures across the countryside, as the trio journey along a desolate highway, Mikal pushes a button, miraculously activating the broken headlights on Eugene’s car. Shortly thereafter, they come upon a man lying in the middle of the dark highway, forcing them to veer off the road in order to avoid hitting him and wrecking the car in the process.
They discover the man, Kneller (Tom Waits), an eccentric commune leader, had fallen asleep while looking for his dog. Kneller invites them back to his camp, where they quickly discover that minor “miracles” occur, as long as the campers remain apathetic about the result. The group stays with the camp longer than intended, and Zia begins to obsess over the miracles and his inability to perform them. When contrasting this to Mikal’s obsession with the people in charge, she reveals that her death was an accidental overdose. Eugene meets a young woman, Nanuk, whom he romances. Just as Mikal and Zia discuss their plans to leave Kneller’s camp, another camper, Yan, emerges from the woods with news that Kneller’s dog has been abducted by a cult leader called “Messiah King” (Will Arnett). Kneller, Zia, Mikal, and Yan set off in search of King and Kneller’s dog.
The group soon find themselves lost and decide to make camp for the night. Unable to sleep, Mikal and Zia discover a nearby ocean shore, where they kiss and spend the night together. In the morning, Kneller discovers them lying among a seashore of used condoms and hypodermic needles. The group eventually reaches King’s camp, where they discover that King is readying himself for a “real” miracle – to separate his soul from his body. As Kneller confronts King, Zia discovers that his Desiree is a devout cult follower, having taken her own life for the purpose of following King into the afterlife.
As King is about to perform public, ritual suicide, Kneller reveals himself to be an undercover agent for the people in charge. King and Desiree are taken away, while Mikal leaves with them, promising Zia that she’ll return. As Zia waits, Eugene and Nanuk arrive, explaining that Mikal has been returned to life and Kneller’s camp has been shut down. They depart together on a train, giving Eugene’s car to Zia. After finally performing a miracle – creating a star in the sky with a lit match next to one that Mikal had created earlier – Zia enters the black hole under the car seat.
In a large warehouse filled with halls of boxes, Kneller is seen picking up Zia’s file from a box, placing it into his inside breast pocket, and commenting on how fortunate it is to know people in high places. Zia wakes up in a hospital bed. He turns his head, noting his parents outside talking to doctors. When he looks at the person in the bed next to his, he sees Mikal. Both look at each other and smile, as the film comes to an end.