Eli Miller is a young boy suffering from a rare disease that causes severe allergic reactions to the outdoors, forcing him to live his life in protective gear. His parents, Rose and Paul, have taken him to Dr. Isabella Horn's secluded medical facility, a large, old house that has been modernized and quarantined. Eli is initially overjoyed that the facility allows him to remove his "bubble suit", embrace his parents, and enjoy comforts previously denied to him. His joy is short-lived, however, as he begins to experience supernatural phenomena in the house. He also begins his treatments, which are excruciatingly painful. The specters repeatedly leave him the message lie, and Eli wonders if they are trying to warn him about Horn's treatments.
Eli befriends Haley, a young girl with whom he speaks through a large window in the house's first floor. She is the only person who believes his claims that the house is haunted. She tells him none of the other patients Horn treated left the facility, implying that they died. Eli discovers the word "lie" is actually the inverted number 317, the passcode to Horn's office. When he investigates the office, he finds Horn's records of past patients, showing that all of them were killed by the third final treatment.
Eli unsuccessfully tries to persuade his parents that they need to leave the facility but his father tries to drug him into unconsciousness. Hurt and confused, Eli barricades himself in Horn's office. He finds a photograph of Horn and her assistants dressed as nuns, and a hidden passageway to an underground room with religious paraphernalia. Horn locks him inside and he experiences an allergic reaction and passes out. When he awakes, he finds he can breathe fine, and he actually has no disease. Rose, feeling guilty for deceiving Eli, goes to him. Eli pretends he's still unconscious. When she opens the gate, he knocks her unconscious with a crucifix and flees but is recaptured by Horn and his father.
His mother regains consciousness and finds a dagger in the crucifix. She also discovers that the stone monument in the room conceals the bodies of Horn's previous patients, bound and adorned with religious symbols. Horrified and angry, she forces her way into the treatment room but Paul subdues her. It is then revealed that Eli is actually a child of Satan, and his "allergic reactions" were manifestations of his emerging powers. Horn begins the third "treatment:" a religious ritual meant to end Eli's life. When she tries to stab him with the sacrificial dagger, Eli uses telekinesis to lift Horn and her assistants in the air, spin upside-down (resembling the Cross of St. Peter), then burst into flame. He also sets the house afire. Eli's mother reveals that she wanted a son so badly, she turned to Satan, who lied that Eli would be a normal child. Paul tries to stab Eli with the dagger to complete the ritual, but Eli interrupts him and uses his powers to crush Paul's skull.
Eli and his mother leave the burning house, where Haley greets them. She reveals that she too is a child of Satan, and that she was unable to tell him, as he had to find and prove his own power. She offers to take Eli to his true father. When he accepts, Haley wonders if Eli can trust his mother. He indicates that he can, and the film ends with Rose driving the two children away from the burning facility.