Tori and Kyle Breyer dream of starting a family, but struggle with fertility. Their wish appears to come true when a spaceship crashes in the woods and the couple discovers a mysterious baby boy whom they name Brandon. As he nears puberty, Brandon appears to be everything Tori and Kyle have ever wanted as he grows to be incredibly smart and helps around the farm, though has never bled and the couple had explained to him that he was adopted out of an agency.
However, as he turns 12 years old, he starts to reach puberty and begins to change. He constantly talks in an alien language and goes to the barn where his spaceship is locked in a storage. While trying to mow the lawn, Brandon discovers his indestructible strength. On his birthday at the local diner, Brandon receives a rifle as a birthday gift from his uncle Noah, only for Kyle to refuse to let him have it. Brandon tells Kyle off and has an outburst, causing the family to leave. He is later shown to have urges for a girl in his class named Caitlyn and sneaks into her room while the family is camping. During gym class when Caitlyn intentionally has Brandon hit the ground during an exercise and publicly calls him a "pervert", he crushes her hand. He receives a two-day suspension, but Caitlyn's mother and diner waitress Erica wants him arrested.
When he walks to the barn's storage again, he breaks the lock chain and discovers the spaceship calling to him and hovers above it. Tori gets him to stop only to be cut on his hand when he falls and Tori explains how he was found. Brandon is upset by their lie, storms out of the barn, and tears apart the family photos, declaring his hatred for his adopted parents. He later goes to see Caitlyn in her bedroom and explains to her that he has discovered that he is "special" and plans to show the world that. He leaves behind a flower on her laptop and goes to the diner in a mask where he pierces Erica's eye with a piece of glass, laser beams his way into the freezer, and kills her off-screen. The police led by Chief Deputy Deever are investigating Erica's disappearance at the diner and Deever discovers a strange symbol on the glass windows. Brandon then sneaks into Noah's closet with the mask and tries to take him home, only to disappear and reappear to telekinetic push Noah to his house. Brandon disappears again and Noah drives away in his truck in fear. He is stopped by Brandon and uses telekinetic powers to lift and drop the truck with Noah in it to the ground, causing Noah to have his jaw torn off from his face when smashing onto the wheel. As he dies, Brandon uses Noah's blood to make the same symbol from the diner windows.
Tori and Kyle become incredibly scared and concerned for Brandon. After pushing Kyle to the wall for confronting him and figuring out he might be behind the recent events, he and Tori decide to have Kyle shoot him in the woods in the guise of a hunting trip. When the two leave, Deever arrives to the Breyer house and asks Tori about the symbols used after Erica and Noah's death, only for Tori to ask him to leave. Tori rushes to Brandon's room and discovers his journal filled with these symbols as well as drawings of his murderous actions to Erica and Noah. In the woods, Kyle quietly prepares the same rifle Noah gave Brandon for his birthday and shoots him in the head. Brandon is unharmed and turns around to Kyle and disappear. Kyle runs only for Brandon to catch him and laser through his head. When Tori tries to call Kyle, she hears Brandon on his phone and tells her that Kyle is gone and he is home. Tori calls 9-1-1 and Brandon tears apart the house. Deever arrives with his partner in shock. Both officers are killed in the house and Tori runs to the barn. She enters the storage and discovers Erica's dissected body with the symbols drawn around her. When Tori finds Brandon, she tells him that he is a blessing and regardless of his actions, she knows there's good in him. However, when Tori tearfully hugs him, she attempts to stab him with a shard from the spaceship and is caught. After attempting to apologize to him, Brandon flies up into the sky carrying Tori and after a short glare, he drops Tori to her death. Right after, a passenger jet hits Brandon.
The next morning, it is discovered that the airplane crashed into the Breyer farm with all 268 passengers killed with a blood drawing of the symbol on the plane. Brandon is seen being cared for in the back of an ambulance and the movie ends with news footage of similar alien deconstructions shown during the end credits.