The soft glow of a television lights up a dimly lit motel room, reporting on the unsettling case of a missing boy named Alton Meyer (Jaeden Lieberher), who was last seen with a man named Roy (Michael Shannon), traveling in a primer gray Chevelle. As the night deepens, Roy removes the duct tape covering the peephole and tells Lucas (Joel Edgerton) that it's time for them to leave. They approach Alton, who is engrossed in a comic book while cocooned under a bed sheet, sporting headphones and dark swim goggles. Together, they venture out of the room.
Meanwhile, the motel's front desk clerk observes the strange trio climbing into the Chevelle, while news of the missing boy continues to play on the television. She is promptly on the phone, her eyes fixed on them as they drive away.
Elsewhere, Calvin Meyer (Sam Shepard) urgently informs Doak ([Bill Camp]) that they must retrieve Alton, no matter the cost. They step out to a gathering of a large congregation that appears to follow a cult-like lifestyle. Calvin's recitation of scripture resonates chaotically, sounding more like a series of enigmatic dates and numbers. Suddenly, an FBI raid disrupts the congregation's proceedings, and we learn they are entangled in a Waco-like cult environment. Authorities round up the congregation members into school buses, leading them away.
As the chase intensifies, Roy and Lucas learn via their police scanner that the authorities are searching for their vehicle. Through the darkness, Lucas dons night-vision goggles, turning off the headlights as they speed through several counties. Roy urges him to switch the lights back on, but not before they narrowly avoid a collision with a stalled car, causing a nearby vehicle to crash. In a tense moment, Lucas exits to check on the driver, just as a State Trooper arrives. The trooper's intentions turn dangerous when he receives the update about the Chevelle; Lucas, acting in desperation, fires at him while narrowly escaping in the vehicle.
Inside the compound, the FBI interrogates congregation members regarding a cache of weapons. Calvin argues that their ownership is still legal, revealing a troubling truth—he is Alton's adoptive father, while Roy is his biological father. Enter Paul Sevier (Adam Driver), an NSA agent who probes into Alton's extraordinary abilities. Calvin remarks that Alton has spoken in tongues, offering a series of classified numbers that also captivate Sevier's attention.
Roy, Lucas, and Alton eventually find refuge at the home of a former congregation member named Elden ([David Jensen]). While attempting to keep Alton safe, Roy is met with alarming circumstances—Elden gazes into the glowing light emitted from Alton's eyes, which sends everyone into a protective frenzy. After collecting Alton in the stolen van, a moment of levity ensues as Alton engages in deep discussions about Superman and Kryptonite, drawing criticism from Roy who wants to shield him from fiction.
Their adventure leads them to a gas station where Alton witnesses fiery debris falling from the sky, prompting an urgent escape as a catastrophic explosion engulfs the area. They seek shelter at Sarah ([Kirsten Dunst]), Alton's mother, who is understandably worried about her son's condition.
As the fallout from the explosion unfolds, the government learns of a satellite incident, indicating that Alton's power may hold pivotal significance. With escalating tensions, Doak and Levi, armed and sinister, trace Sarah's movements, while Lucas reveals his past connection with Roy as a former State Trooper before descending into Calvin's cult.
Tragedy strikes when a vehicle ambush occurs, capturing Alton and leaving Lucas, Roy, and Sarah fighting for their lives. They find themselves cornered by a military blockade and witness the shocking sight of a helicopter leaving with Alton. This prompts a desperate escape into the woods, where Alton reveals his need to embrace daylight, seemingly healing under the sun.
As the authorities decode Calvin's cryptic sermons, revealing coordinates that align with the chaotic events they’ve encountered, Alton's confidence grows. He shares his extraordinary vision with Lucas, transforming their perception of reality, while critical decisions unfold nearby. Just as all seems lost, an astonishing spectacle occurs: a dome encircles Alton, revealing a realm of light and energy, a parallel existence unlike our own.
In the aftermath of their harrowing journey, Lucas faces government scrutiny while Sarah adapts her appearance, likely to evade capture. Roy, stripped of his freedom and left in despair, feels the remnants of Alton's light as he stares into the sun, giving a glimmer of hope that their story may not be finished just yet.
