Sam Temple is sitting in his high school history class, half-listening to a lesson on the Civil War, when his teacher suddenly disappears. Sam looks around the classroom to make sure he isn't dreaming, but others saw it happen as well. A student named Josh has also vanished. Astrid Ellison, a genius and the girl Sam likes, enters Sam's classroom to see if anyone has seen her teacher and fellow students. They also have disappeared. Kids empty out of their classrooms, trying to figure out what happened. Panic sets in for some when they realize that, although there is electricity, television and cell phones aren't working.
Sam, his best friend, Quinn, and Astrid go home and search for their parents. They soon realize that no one over the age of 15 is left in their town. Sam is afraid to show his friends the strange light in his room that hovers in front of his closet. It appeared after a violent thunderstorm and has been there for two nights. He knows the light might have something to do with the weird happenings, but he's afraid his friends will blame him for all the disappearances.
Astrid finds a journal entry on Sam's mother's laptop. It indicates that she had witnessed some strange things happening in Coates Academy, the school where she worked. Sam's mom didn't mention this to anyone because she didn't think anyone would believe her.
Sam and his friends head back to the center of town because they think other kids will congregate there. A fire has broken out in an apartment building, so Sam calls out orders, sending some kids to warn the nearby day care and getting others to go to the hardware store and fire station to get hoses. A child's voice cries out from the apartment. Sam goes in to rescue her. The fire and smoke nearly overwhelm him, but he finds the little girl. She is terrified by Sam's ash-covered appearance. She raises her arms, and a stream of fire shoots from her hands. She narrowly misses Sam; when she tries again, he defends himself with a beam of light from his hands. The girl falls to the floor. Sam scoops her up and pushes her out of a nearby window where others grab her. They help Sam out as well. Unfortunately, the little girl is dead. The others believe she died from smoke inhalation, but Sam believes he killed her with his strange new powers.
The kids in the plaza seek Sam's advice on what to do next, which makes him uncomfortable. Astrid can't find her autistic brother, Little Pete. She thinks her mom might have taken Pete to work with her, to a hotel outside of town. Sam and Quinn agree to help her in her search. They don't find Little Pete, but they do discover a barrier cutting through the tennis court, spreading out through the pool and into the horizon. The barrier is opaque, but they can see the sky through it. A tennis ball bounces off it, but when Sam touches it, it burns him. Since night has fallen, the three decide to sleep at the hotel where her mom worked before heading back into town.
Lana Lazar's grandfather is driving her home when he disappears from the behind the wheel of his pick-up truck. Lana and her golden retriever, Patrick, plummet down a cliff. She is severely injured by the crash and cannot move or get help. That night, a mountain lion tries to attack her, but Patrick fights off the animal. Her dog is injured and bleeding, but Lana can do nothing but put her hand over the wound. Hungry, tired, wounded and sobbing, Lana falls asleep. When she wakes in the morning, Patrick is healed. She soon realizes that she cured the dog. She spends the rest of the day healing herself so she can find help.
Back in town, some of the older children try and maintain order. A girl named Mary and her brother struggle to take care of the babies and toddlers left in the day care center. Eventually Mary seeks Sam for help. When she finds out he's left, she enlists another boy, Howard, and his bully friend Orc to get supplies for the day care kids.
The next morning, Sam and his friends find another boy, Edilio, trying to use a backhoe to dig under the barrier, but to no avail. Sam realizes that people on the other side of the barrier, in the rest of the world, have better resources to break through it. It is futile for them to keep searching for a way out. Astrid asks Edilio to join them in the search for her brother. She wants to go to the other side of town, to the nuclear power plant where her father worked. Edilio suggests they take one of the hotel's golf carts instead of walking. They take a path that skirts around the town to avoid wasting time by talking to people. Still, Howard, Orc and several other bullies try to flag them down. When Sam and his friends don't stop, the bullies get a truck from a gas station and chase them. Once they are caught, a fight ensues, but Astrid convinces the boys to stop. Howard tells them that Orc has been put in charge of the town, or FAYZ, since Sam left the night before. FAYZ stands for Fallout Alley Youth Zone. The bullies demand the golf cart before they'll release Sam and his friends.
Sam, Astrid, Quinn and Edilio make it to the power plant. Since Edilio is a recent transplant to the city, Astrid tells him how a meteorite hit one of the power plant's towers almost 15 years ago. The meteorite drilled most of the uranium from the tower into the ground so there was fallout from the accident. Astrid finds her little brother playing his video game in the control room. They discover a map of the area on one of the consoles. The power plant is in the center of a red circle that surrounds the nearby area. It seems to follow the barrier the kids have seen. Astrid doesn't think there's been a radiation leak because none of the alarms are going off.
They decide to spend the night in the control room, but when Sam wakes up and accidently knocks over a display case, the loud noise triggers a fit from Little Pete. As Pete screams, Sam starts to choke. The others are too busy trying to calm Pete down to see the trouble Sam is in. Finally, Sam stretches out his hand, and a brilliant light flashes. Sam falls unconscious, and Little Pete stops screaming. The others are petrified. They insist on leaving the plant immediately. When they stop to rest, Edilio insists Sam confess the truth about his strange powers. Sam admits that it happened twice before. Once when he made the ball of light appear in his room and once several months ago. Sam had been woken up by his mom and stepfather arguing. When he saw his stepfather with a knife, he panicked, and the light shot from his hand, burning his stepfather's arm.
Astrid admits that Little Pete has weird powers, too. He can transport people through walls to other places. The others wonder if he had something to do with the disappearing adults. They all agree to keep Sam's and Little Pete's secrets as they return to town.
The following day, four cars carrying students from the Coates Academy arrive in the plaza. The Academy is a boarding school for troubled kids. One of the students, Caine Soren, makes a speech entreating the town kids to come together to talk things out with the Coates students and make a plan for the future. The groups meet in the Catholic church in the plaza. Caine introduces a small boy named Computer Jack who will help get a communication system up within the FAYZ. He then nominates his friend Drake to be sheriff and Sam to be fire chief. When Caine tells Orc and Howard that they'll be in charge of supplies, the bullies get angry. Before they can battle, a giant crucifix flies off the wall and smashes into the pew where the others had been standing. It misses Orc and Howard but hits another boy. The meeting is adjourned until the injured boy can be helped.
Caine and his cronies take up residence in the town hall. One of his helpers is a girl named Diana; she is able to "read" the other kids and tell if they have any powers. Caine is making Computer Jack keep a list of the kids and what supernatural strengths they have. Drake, the new sheriff, uses his natural strength to intimidate, and in some cases physically punish, those he thinks are defying him.
Sam, Quinn and Edilio make their home in the firehouse. The following day, a girl falls into their threshold, bleeding. Orc comes up behind her with a bat. When Sam and his friends intervene, Orc tells them that she's been breaking the law. Sam still won't let Orc beat her anymore. The bully prepares to hit Sam with the bat, but Edilio knocks Orc down. The two fight until Drake arrives. He calls for everyone to stop, but Orc keeps kicking Edilio. Drake pulls the bully off and beats him.
When he questions what happened, another Coates student tells him that the girl was using the power. Drake immediately stops him from saying more, but a town kid pipes up that she was doing magic tricks, making small balls of light float from her hands. Orc says he ordered her to stop. Drake tells the gathered crowd that since Orc is a deputy sheriff, he has to be obeyed. Drake defends using physical force as a way to make everyone obey the rules. When Edilio questions what the rules are, Drake tosses him a crumpled piece of paper. Drake, Orc and the others leave the firehouse.
Sam, Edilio and Quinn bandage the wounded girl and take her home. Later they read the rules Drake gave them, which basically say that Caine has control over the FAYZ and Drake is his enforcer. That night, the injured girl dies.
Lana struggles throughout the day and finally finds a place to rest, an isolated cabin in the middle of the desert. Fortunately, the hermit who used to live there stockpiled food. That night, Lana hears something scratching at the door. A gravely voice begs her to come outside. She convinces herself that she's imagining things. The cabin has no restroom, so eventually Lana runs to the outhouse. On the way back, a coyote blocks her way. Her grandfather always assured her that coyotes would back down if you showed aggression, but when she yells and waves her arms, the animal doesn't move. Instead, she sees several more running to join it. Realizing that she must reach the cabin or she'll be attacked, Lana bolts toward the door. Some other creature flies toward the coyote, causing it to jump back far enough for Lana to reach the cabin. In the morning, she finds a dead coyote, but also a dead rattlesnake. She's confused because she was certain she saw the snake fly.
Sam, Quinn and a younger girl are assigned to check houses for any small children or pets. Sam is appalled when he finds the body of a toddler he knew. He feels he should have remembered to check on the boy. Sam and Quinn, who have been arguing for the past week, fight outside the dead boy's house. Sam feels Caine can't be trusted while Quinn thinks he's OK and wants Sam to stop trying to be a hero. Quinn takes the boy's body back to the plaza while Sam checks on his own home. It has been ransacked.
His mother's laptop is gone as well as a box in which she'd locked several important documents, including Sam's birth certificate. Sam never knew his real father and never bothered to look at the certificate to find his name. Sam knows it was Caine who took his mother's things. Caine would also have seen the light in Sam's room and figured out that he has powers, too. Sam wants nothing more than to confide what has happened to Astrid, with whom he has started a romantic relationship.
On his way back into town, Sam meets some old friends from school, Emma and Anna. These twins are helping with the preschool children, taking them down to play at the beach. As they say goodbye, Emma jokes that he needs to wish them a happy birthday. He starts to leave and then realizes what she said and hurries to catch up with them. No one knows what will happen when they reach their 15th birthday. Anna senses his fear when she admits they'll be turning 15 any moment. Before Emma can calm her sister down, she disappears. Anna begs Sam to hold her hands and keep her with him, but six minutes later, she blurs in his vision and disappears.
Drake witnesses this episode and runs back to tell Caine. Caine is concerned because his birthday is less than a week away. Diana has been reading Sam's mother's diary and found something interesting. She gets Drake to break the lock on the box they took from Sam's house. Inside, she finds something to confirm her suspicions — Sam's birth certificate. It confirms that Sam was born on the same day as Caine, only three minutes apart. She believes Caine is Sam's twin brother. Caine is angry to think that his mother gave him up for adoption while keeping Sam.
Sam finds Astrid and tells her what happened to the girls. He's scared that the same thing will happen on his birthday. He plans to look for a way out of the barrier. When they go to the grocery store to scavenge for food, Drake hits Sam with a baseball bat and someone puts Mylar balloons over his hands. He is taken to see Caine, while Drake holds Astrid and her brother hostage. What hurts Sam more than the wounds inflicted by Drake is the knowledge that Quinn told the gang where to find him.
Caine tells Sam that they are brothers and then uses his telekinetic ability to throw Sam across the room. Before he can get answers from Sam about their parents, Drake bursts in. Astrid and her brother have disappeared. Caine is frantic when he figures out that Little Pete may have more power than he does. He orders Drake to find and kill them. Orc and Howard carry Sam into the school weight room where they tie him to a weight bench. They force him hold a heavy barbell over his neck and then leave him. If Sam tries to get the Mylar off his hands so he can use his power, the bar will press down on his neck, choking him. He struggles to free himself for several minutes before Quinn arrives and helps him escape. Sam accepts his help but does not forgive his earlier betrayal.
Although Little Pete transports them back to their house, Astrid knows they won't be safe there for long. They have to find somewhere else to hide. She is also haunted by the fact that Drake threatened her and hit her until she called Little Pete names. It was her fear and stress that made Little Pete transport them. She decides to hide out in her mother's hotel, hoping that Sam will look for them there.
Sam and Quinn pick up Edilio and set out for the marina. Sam thinks Astrid has gone to the power plant, and he wants to take a boat to save time. They are chased by Orc, Howard and another boy, but manage to get away. Sam gets Quinn to tell the others that they're headed for the power plant. Sam punches Quinn and then lets him know that they're actually going to the hotel. However, Drake has climbed the church steeple, looking for Astrid. He sees Sam turn the boat around and head for the hotel. He sets out to find her first.
Astrid is trying to find food for her brother when she hears the elevator start up. She senses trouble and tries to get one of the doors to one of the rooms unlocked. She is able to slip inside just as Drake exits the elevator. He shoots several times through the door but misses her. Astrid manages to get herself and her brother to the balcony below the room Drake is attacking. She hopes Drake will think they transported again. Her plan works until Little Pete moans. Drake takes aim at them, but before he can shoot, Sam smashes him over the head with a table lamp. Sam, Astrid and the others try and escape in the boat but are pursued by Howard and Orc, until they crash into the barrier.
Lana finds gold bars in the cabin and deduces that the hermit who lived there must have been a miner. She hopes to find his truck in the nearby hills so she can use it to get to civilization. She finds the truck in the mine, but no keys. The coyotes arrive. Their pack leader has mutated so he can talk and tells her that she must die. They attack and bite her but then stop. Instead of killing her they force her to walk deeper into the caves. A powerful presence overwhelms her mind, causing her great pain until she eventually passes out. The coyotes drag her from the cave. They force her to run with them. The Darkness she encountered in the cave wants her to teach the coyotes about humans so they can kill them. Lana finally coerces the coyotes into taking her back to the cabin so she can get some human food.
Back in town, Caine wants to return to Coates Academy to set up video cameras. He knows it is time for Andrew, one of his cronies left back at the Academy, to turn 15. Caine wants to tape his vanishing, then analyze the video to see if there's any way to stop the process. When they arrive back at the school, a gruesome sight greets them. Kids, their hands encased in cement blocks, come stumbling outside. They are filthy and starving. They beg Caine and the others for food. Before Caine can enter the school, a loud boom is heard; the sound waves push him back. Caine uses his powers to throw bricks at whoever is trying to stop them from entering. It turns out to be Andrew, the boy they've come to watch disappear. Caine restrains Andrew so he can't move while the process takes place.
Sam and the others have beached their boat on shore. They follow the barrier for a while but soon realize it has no end. It reaches to the sky, and the kids can't tell if they are seeing the actual sky or its reflection. Sam decides he can't waste the few days he has left. He can't find a way out, and he can't hide from Caine anymore. He must face the bully before they both disappear. He and his friends trek across the desert throughout the day, heading back toward town. As night falls, they find a cabin. A voice nearby tells them to get inside. Lana runs into view with Patrick alongside her. She tells them again to run, but the coyotes are already attacking the others. Sam and his friends manage to fight off the coyotes and get into the house, but not before Sam is seriously injured. Lana uses her powers to heal him. The children barricade themselves in the house to prevent the coyotes from getting in.
Back at the Coates Academy, Caine and his cohorts secure Andrew to a table so he can't move anything but his hands. Computer Jack sets up cameras so they can videotape his vanishing from all angles. Andrew prays to God to forgive him for being cruel to the other children. Then he sends sonic waves of energy out around him in hopes that it will keep him from disappearing. The time recorded on Andrew's birth certificate passes, and still he remains on the table. He keeps up the sonic waves for 30 seconds.
When he finally stops, he lets out a prayer of thanks. Then he's gone. When Caine and his group examine the films, they find only two that actually show Andrew's disappearance. For a few frames, the ropes are gone from his arms and legs, and he seems to be reaching toward a flare of light. He has a smile on his face. When Jack zooms in on the light flare, they can see something like a hole surrounded by teeth. Caine figures that something disguised itself to make Andrew reach for it. He vows that when it's his time to go, he won't take the bait.
Sam, Lana and the others are locked in the cabin when the coyote pack leader returns with a lit torch. Lana knows that The Darkness gave it to him. The children must flee the cabin and face the hundreds of coyotes waiting outside for them. Sam has learned how to summon his power. He uses it to attack the first wave of coyotes, setting them on fire. They flee into the rest of the pack, setting off a panic. Sam and his friends are safe for the moment, but they must find their way back to town. They come across one of the Coates students with her hands in concrete. When they try to help her, Drake descends on them. He has set a trap, and the others have walked into it. He takes them to the Academy to face Caine.
First, Drake takes his prisoners into a common area where they see other kids, whose hands have been encased in concrete, eating from trays like pigs at a trough. Drake threatens to shoot Astrid if Sam doesn't get his hands put in concrete as well. After Sam's hands begin to set, Drake makes Astrid do the same thing. Astrid cries hysterically, trying to convey her terror to Little Pete. When Caine and Diana arrive, Sam distracts him from what Astrid is doing. He tells Caine that Lana is a healer. To prove her powers, Caine has Drake shoot Sam in the leg. As Sam collapses, Astrid knocks her brother's video game from his hands. Before her concrete block can crush it on the ground, Pete causes all the concrete blocks to disappear. Caine and Diana run into the school while Sam uses his power to burn Drake's arm so he can't shoot Little Pete. Sam, his friends and the Coates students who had been tortured, make their way back to town.
Sam gives a speech uniting all the town kids and the Coates students, offering them a new beginning to work together to fight Caine. He sends Edilio on a special secret mission while Astrid goes among the children to find out if they have any powers. Though tired, Lana spends her remaining energy healing anyone who's wounded.
Drake's arm must be amputated. Once he is coherent, Caine sends him into town to kidnap Lana, which he does. He comes across Orc and Howard on the road back to Coates. The coyotes attack the group. They want Lana. Drake refuses, threatening to shoot the pack leader and any other animals that try to take her. The coyotes take Drake and Lana with them to The Darkness. They leave Orc behind.
Edilio has returned from his mission. He gets Astrid and her brother to follow him to the firehouse where he and Sam show her the security tape from the power plant. She sees her father and several co-workers interacting with each other. Suddenly a loud alarm sounds, and the adults frantically search their monitors. Other adults arrive. Little Pete can be seen holding his ears and rocking. His father pushes him away when Little Pete tries to approach him. Pete ends up sprawled in front of a monitor flashing the number 14. Astrid explains that the number is a code that means there's a core meltdown in process. She watches as her brother pulls his hands from his ears, and a moment later, a bright flash of light obliterates the picture.
When it comes back on, the sirens are silent, the adults are gone, and Pete returns to playing his game. The time on the tape is the same moment when every other person over the age of 14 disappeared. Astrid pleads with Sam not to share this information, convinced her brother didn't know what he was doing. Sam explains that Little Pete is a hero, that he saved them from a nuclear holocaust.
The coyotes take Drake and Lana into the mine to see The Darkness. The Darkness possesses Lana's body and uses it to speak. It searches Drake's mind and knows he will help The Darkness destroy the others. The Darkness uses Lana to reform Drake's stump into a whip-like tentacle. The Darkness instructs the coyotes to heed Drake's commands. Drake and the coyotes return to Caine and prepare to attack Sam and the town.
In the battle that follows, Drake and the coyotes take Mary and the preschoolers hostage. Drake will let the coyotes eat the little children unless Sam gives himself up to Caine. Sam agrees, but only in theory. One of his soldiers arrives at the day care with a tray overflowing with raw hamburger. The coyotes set on it in frenzy. Sam uses his power to light them on fire. Drake attacks Sam, using his whip-arm to choke him, but Quinn takes aim from a nearby rooftop and shoots Drake. Although he misses, the shot is enough to frighten Drake. He leaves. Sam gets some of the town kids to pretend to surrender to Caine in the plaza.
Unfortunately, Caine sees the coyotes fleeing as he and his cohorts drive into town. He convinces the pack leader to follow him and attack the children in the plaza. Sam uses his power to fight the coyotes off, but there are too many of them. They set upon the children in a desperate need to feed. Caine arrives and threatens to use his power to destroy the church where Astrid and many other children are hiding. Sam and Caine fight power-to-power, destroying property and maiming each other. Caine causes the church to collapse on Sam. Drake returns to town, eager to rejoin the battle, but Orc stops him. The former bully has morphed into a rock beast and blames Drake for his predicament. The two fight each other.
Diana tries to get Caine to call off the coyotes, now that she thinks Sam has been killed, but he refuses. He is too engrossed in watching Orc and Drake fight. A bright light glows from the church, and Sam emerges from the rubble. Caine hides behind Astrid, taunting Sam to try burning him and risk killing her as well.
The world around Sam fades as the exact day and time of his birth arrives. His mother appears and begs him to follow her. Although tempted, Sam refuses, wanting to stay and help Astrid instead. Caine enters the eerie light, and Sam's mother calls to him as well. Both boys refuse her, and her appearance shifts into that of a giant mouth ringed with teeth. It mocks Caine, telling the boy that they will meet again in the future. The creature melts away and both boys are sent back to the real world. Sam allows Caine to live if he agrees to leave the town. Caine vows to return. He takes Drake and Diana with him and leaves. He asks the pack leader to take him to The Darkness.
Those that survived the battle gather together to celebrate Thanksgiving. Sam encourages the children to have hope that things will return to normal one day. Until then, he asks that they all work together to make the world they're living in a good one.