Eli is a sixteen-year-old boy who has spent the last six years living inside an underground compound built by his billionaire father. Haunted by his actions on the night his family fled into the shelter, Eli isolates himself entirely, refusing to let anyone touch him and relying on a grueling exercise regimen to cope with his shame. He monitors the family's dwindling food supply and gradually begins questioning his father's explanations about the outside world.

Rex is an eccentric, highly driven billionaire and former computer science prodigy who built the Compound to protect his family from a nuclear attack. He exerts intense control over the environment and his family members, establishing rigid routines while keeping critical information locked away. His obsession with survival metrics often makes him appear cold and calculating, even to his own children.

Clea is a world-class cellist who surrendered much of her independence when she married Rex. Inside the Compound, she frequently serves as a peacekeeper while quietly managing her own anxieties about their prolonged confinement and her consecutive pregnancies. She slowly begins to notice inconsistencies in her husband's stories, pushing her toward subtle acts of defiance as conditions worsen.

Lexie is Eli's adopted older sister, characterized by her materialism and deep desire for her father's approval. She embraces the life Rex has provided them, often aligning herself with his worldview and defending his choices against her siblings' criticisms. She views herself and Eli as being similar to their father, prioritizing self-preservation over sentimentality.

Terese is Eli's younger sister, nicknamed "Little Miss Perfect" for her strict adherence to routines and her mastery of skills like playing the oboe and speaking French. She is highly perceptive and becomes the first family member to voice concrete suspicions about their father's narrative. Her kindness and empathy painfully remind Eli of his missing twin brother.

Eddy is Eli's twin brother, remembered as kind, generous, and universally beloved by those who knew him. He was left outside the Compound during the family's panicked escape when he returned to the cabin to retrieve medicine. His absence forms the emotional core of the family's grief and serves as the primary source of Eli's intense self-loathing.

Gram is Clea's mother and the children's grandmother. She is remembered as the only person willing to openly argue with Rex's dominating personality and push back against his immense wealth and control. Her absence in the Compound weighs heavily on the family, as she was locked out alongside Eddy when the silver door was sealed.

Phil is Rex's trusted accountant and business associate from the time before the nuclear event. Through Eli's memories, Phil is characterized as someone who recognizes Rex's manipulative tendencies but remains deeply entangled in his billionaire employer's vast financial and logistical enterprises.

Lucas is a young boy born inside the Compound, part of the group of children kept in a room behind a yellow door. Innocent and playful, Lucas bears a striking resemblance to Eddy. His presence forces Eli to confront the reality of the family's dire situation and isolation.

Quinn is another of the young children born to Clea while living inside the Compound. Kept in the isolated yellow room, Quinn's innocent physical touch profoundly affects Eli, who has starved himself of physical contact for six years out of guilt.

Cara is one of the youngest children born inside the underground shelter. She is kept separate from the primary living areas of the older siblings for much of the novel, though her older sisters attempt to integrate her into basic household routines.