Jacob Rathbone, a 12-year-old boy grappling with a profound fear of darkness, lives with his stepfather, Davis and his mother, Isabel. The constant strain of his distressing night terrors leaves Isabel feeling frustrated and overwhelmed. After an incident where Jacob is discovered dancing in his late grandmother's dress, he faces bullying at school, resulting in suspension. Consequently, he is sent to a boarding school in the wilderness, run by the quirky couple, Dr. Sherman and Mrs. Sherman.
At the school, Jacob encounters a group of classmates, including the twins Lenny and Calvin, alongside outcasts like the disfigured burn survivor Phil, Frederic, who suffers from Tourette's, and Elwood Ramsay, who is autistic and is often manipulated by Christine Holcomb, the daughter of Mr. Holcomb, whom Jacob met at a previous dinner. The strict environment of the school is punctuated by Bible studies and harsh corporal punishments.
Tragically, the tension escalates when Frederic is found dead in what appears to be a suicide by hanging. Seizing the moment, Christine attempts to escape with Jacob but is soon caught. Dr. Sherman reveals a dark secret: Christine had previously murdered her brother, Timothy, leading to her mother’s suicide. In a chilling confession, she admits to coaxing Frederic into dangerous behavior that resulted in his death. During a tense encounter in her room, she attempts to stab Jacob with scissors but is overpowered, revealing her twisted affection for him.
The situation deteriorates further when Jacob discovers Elwood dead in bed. A heated dispute between Dr. and Mrs. Sherman unveils her true identity as Lynn Adams, and together, they plot to eliminate the children. To Jacob's horror, he finds the remains of the real Dr. and Mrs. Sherman along with Frederic hidden in the freezer. A conversation hints at a grim arrangement where Mrs. Ramsay had sent Elwood there for what would be his fatal "accident," a fate planned for all the children.
The horrors unfold as Ms. Adams murders Mrs. Ramsay, prompting Dr. Sherman to retaliate by killing the groundskeeper. He chillingly reveals to Jacob that he has engaged in contract killings since he was Jacob's age and intends to eliminate everyone in a fire. In a shocking twist, Jacob learns it was Davis who sent him there to rid himself and Isabel of Jacob.
In a desperate fight for survival, Jacob manages to kill Dr. Sherman and ignites a fire to purge the evil haunting the school. He bravely rescues the other children but leaves Christine behind, seeking justice for Frederic's death. As Jacob reveals his true self to his friends, he embraces his identity, signaling a newfound strength.
The film intersperses flashbacks of Jacob's grandmother, Feiga, who persevered through the terrors of World War II, and her friend Tsipi, enduring horrific abuse. The narrative culminates with Jacob overcoming his fear of the dark, only to face a new terror as Isabel’s cries echo from the dinner table. Ultimately, Davis meets his end through poisoned wine, a consequence of Jacob’s past experiences, symbolizing his evolution into a warrior against the darkness.
