The glow of a television set illuminates an otherwise dark motel room. On the news, the story of a missing boy named Alton Meyer (Jaeden Lieberher) last seen with a man named Roy, traveling in a primer gray Chevelle.
Roy (Michael Shannon) pulls back duct tape covering the peephole in the door and sees that its night. He tells Lucas (Joel Edgerton) that its time to go. They gather Alton, whose reading a comic book underneath a bed sheet. He’s wearing headphones and darkened swim goggles. They exit the room.
The front desk clerk of the motel watches as the peculiar threesome gets into a Chevelle. The news is on in the motel office too. She picks up the phone as the Chevelle drives away.
Elsewhere, Calvin Meyer (Sam Shepard) tells Doak (Bill Camp) that he must get the boy back no matter what. They exit the room and we see they’re on the altar of a large congregation of religious followers. He starts reading scripture which sounds more like a series of dates and numbers. The FBI raids the church and we see that were in the compound of a Waco-like cult. They gather up the members of the congregation into school buses and take them away.
Through their police scanner, Roy and Lucas discover the authorities have a description of their vehicle. Lucas puts on night vision goggles, turns off the headlines and speeds through the darkness. After driving through three counties, Roy tells him to turn the lights back on and slow down. As Lucas does, their car narrowly misses a stalled car in the middle of the road. However, a vehicle heading in the opposite direction isn’t as lucky and crashes into the stalled car. Lucas stops, gets out and checks on the driver. As he does, a State Trooper pulls up. The trooper is about to assist when he gets a message on his radio about the Chevelle. Lucas pulls his gun and tells the trooper not to do it. The trooper pulls his weapon anyway, so Lucas shoots him, gets back in the Chevelle and off they go. Roy assures Lucas that the trooper was wearing a vest.
The FBI questions the members of the congregation about the large collection of weapons they’ve started to amass. Calvin says it is still currently legal to own guns in this country. We also find out that Calvin Meyer is Alton’s adopted father. Roy is his biological father. NSA agent Paul Sevier (Adam Driver) arrives and questions the congregation too. He asks about Alton’s powers. Calvin tells him that he speaks in tongues and has given the church a series of numbers. It turns out those numbers are classified government information. They also talk about the light Alton has in his eyes. Sevier lets everyone return to their church. Doak and Levi (Scott Haze) gather a secret stash of weapons and head out after Alton.
Roy, Lucas, and Alton get to the home of a former congregation member named Elden (David Jensen). He hides them and already has a darkened room for Alton to sleep. In the morning, the entire house is rumbling like there’s an earthquake. Roy runs into Alton’s room and sees Elden staring in the bright lights shooting out of Alton’s eyes. They pull Elden away and get the goggles back on Alton. Elden explains that he just had to see it one more time. Lucas takes the man’s car and gathers Alton. Roy pulls his gun on Elden and tells him that he has to do this because the man knows too much. He begs Roy to spare him.
Alton reads comic books in the back of Elden’s stolen utility van and asks questions about Superman and Kryptonite. Roy admonishes Lucas for letting him read that. Lucas defends his decision by saying that its good to read. Roy doesn’t want Alton reading stuff that isn’t real. We get the sense that, before all this, Lucas wasn’t a member of the Meyer family like Roy was. Alton starts speaking in Spanish. Lucas is surprised he can do that. Roy says he can’t and turns on the radio. It turns out that Alton is reciting what a DJ is saying on a Spanish speaking radio station even though the radio wasn’t even turned on. Roy was able to determine that the numbers Alton was saying to the church were coordinates with a corresponding date. He needs to get him to those coordinates by that day a few days from now.
They end up at a gas station. Lucas goes inside to get supplies. Roy makes a phone call and tells Alton to stay in the van. Roy tells the person on the phone that he misses them and will see them in a few hours. Something above catches Alton’s attention and he gets out and wanders away to the edge of the parking lot. Roy runs over and Alton apologizes and points to the sky. Fiery debris rains from the sky onto the gas station. Lucas and Roy take Alton, get in the van and drive away as the gas station explodes behind them.
They go to the home of Sarah (Kirsten Dunst). Shes Alton’s mom and concerned that he’s not looking too well. She puts him to sleep.
Re-joining Sevier and Agent Miller (Paul Sparks) from the FBI at the aftermath of the gas station, we find out that a defense satellite in charge of stopping nuclear weapons exploded and crashed at the gas station. There’s a heat reading comparable to a nuclear bomb where Alton was standing when the satellite exploded, but there isn’t any radiation present at the site. They determine they can program a drone to track that same reading, so next time Alton’s superpowers flare, they can figure out where he is.
Doak and Levi, armed with duct tape and guns, pay a visit to Sarah’s mom.
On the radio, the official report is that a weather satellite crashed.
Lucas works on rigging up Sarah’s car with some equipment while she makes small talk. We find out that Lucas was a childhood friend of Roys before he left to join Calvin’s cult. His job before all of this, he was also a State Trooper. Sarah couldn’t handle seeing Calvin raise her child, so she left the cult. Roy bravely stayed behind to keep an eye on Alton.
Doak and Levi go to Sarah’s house and find Elden’s van. Then they go to Elden’s house and find him alive. Roy couldn’t kill him after all. They ask where the heroes are headed.
Our heroes drive and suddenly Alton has difficulty breathing. They pull over and try to help him. Lucas insists they should go to the hospital, but Roy says they cant. If they do, they won’t be able to get to the coordinates. Light shoots out of Alton’s eyes and he can’t control it. They take him out of the car. The grass around him starts to die. He recovers and tells Sarah and Lucas to go. He points to a distant light in the sky the government knows where they are.
Roy and Alton flee into the woods and find a cave. Alton tells Roy that he needs to be outside in the day time. Roy says that could harm him. Alton says that Roy needs to trust him. In the morning, Alton and Roy watch the sunrise. Alton recovers completely and his hand illuminates with light.
Sevier decodes the numbers from Calvin’s sermons. They’re a series of coordinates with corresponding dates. Some line up to stuff like where the State Trooper was shot and where the gas station explosion happened. Others are just government secrets. Putting the government numbers aside, Sevier figures out where our heroes are headed next!
Lucas and Sarah are holed up in a hotel room. Sarah reassures Lucas that Roy won’t stop at anything to get Alton where they need to be. There’s a knock. It cant be Roy and Alton because it is still daylight. Wrong! It is them. Roy says that Alton was able to show him a glimpse of where he needs to be. Alton explains that he belongs with people who live on a plane of existence that’s parallel to ours, but different from ours. He shows Lucas that place through the lights in his eyes. Lucas now believes.
Lucas puts on his Kevlar vest and goes out to get their car. As soon as he opens the door, he’s shot by Doak and Levi. Ray grabs his gun and exits the room too, but he’s shot in the neck. Doak and Levi break in the room and take Alton. They zip tie Lucas, Ray and Sarah and drive away. Sarah breaks free and rescues the other two. They head off after the kidnappers, but the trip is short. They’re stuck in the traffic of a military roadblock. Ray goes off-road to get to the front and there they see a military helicopter flying away from Doak pick up. Inside the open truck, the blanket that Doak used to cover Alton’s head. It’s over.
At a military compound, a group of military leaders and scientists try to talk to Alton. He could be a valuable asset. He says that he’ll talk to Sevier and only to Sevier, so everyone else leaves. Using telekinetic powers, Alton makes it so that the security cameras aren’t recording the actual present events. He telekinetically opens the door which imprisons him. Sevier sheepishly goes inside to talk to Alton. Alton shows him his light.
In the middle of nowhere, Roy is devastated that he failed. Then all of the nearby payphones start ringing at once. He picks up. On the other end, Sevier tells him that he has Alton and tells Roy where they can meet. Alton magically helps Sevier steal a car. In the morning, Sevier turns over Alton to Roy and Sarah. He handcuffs himself with Lucas cuffs and asks if Lucas would be willing to punch him which Lucas has no interest in doing.
Alton tells Roy that there’s one route they can go to get through the government roadblocks keeping them from their final destination. Roy and Sarah also come to terms with the fact that Alton might not belong with them after all and that once they get there its goodbye. They drive through a small military blockade on a country road. Alton and Sarah get out of the car and run through swampland. Roy and Lucas keep the military occupied while driving in Sarah’s, now badly damaged, car.
As if by magic, a dome appears around Alton that takes up a good third of the United States. Everywhere, everyone sees this magical world where Alton belongs. All of the beings that inhabit that world are made of light that comes from their hands and eyes, kind of like an evolved version of Alton. Lucas and Roy’s car crashes. Alton and Sarah share a goodbye glance and then as suddenly as everything appeared, it, along with Alton disappears.
Lucas is being questioned by the government. His incredible story is the only story he has to tell. Sarah cuts her hair in a scummy bathroom clearly on the run. Roy is in prison. He has electrodes on his head and stares into the sun. His eyes magically illuminate like a lesser version of Alton’s.