Brad (Sam Rockwell) and Abby Cairn

Brad (Sam Rockwell) and Abby Cairn (Vera Farmiga), are an affluent New York couple with two children. Their firstborn, 9-year-old Joshua (Jacob Kogan), is a child prodigy to such a degree that he thinks and acts decades ahead of his age. He is nearly always clad in conservative business attire and demonstrating limitless brilliance as a pianist with a marked predilection for "dissonant" classical pieces.

Joshua gravitates toward his aesthete uncle Ned (Dallas Roberts) as a close friend, but distances himself from his immediate kin, particularly following the birth of his sister Lilly. As the days pass, bizarre events transpire as the mood at the house regresses from healthy and happy to strange and disorienting. As the baby's whines drive an already strained Abby to the point of a nervous breakdown, Joshua devolves from eccentric to downright sociopathic behavior.

Joshua causes a fight between his mother (who is Jewish, but non-religious) and paternal grandmother (who is a Christian and who constantly proselytizes Joshua) when he tells his parents he wants to become a Christian. Abby gets very angry and swears at the grandmother, telling her to leave her house immediately. Joshua later convinces his mother to join him in a game of hide-and-seek. As Abby counts to fifty, Joshua takes his baby sister from her crib to hide with him, causing his mother to panic and pass out while searching for them in the empty penthouse above them, before he puts the baby back into the crib to make it look as though his mother was hallucinating the entire incident.

Later, after discussing Abby's psychological problems with his brother-in-law Ned, Brad takes two weeks off from his job to look after Abby and his children. When he arrives home, Joshua has gone to the Brooklyn Museum with his sister and their grandmother Hazel (Celia Weston). Joshua frightens his grandmother by describing to her in detail about Seth, the Egyptian God of Chaos, and his violent acts. While they are at the museum, Brad watches a video tape of Joshua scaring his baby sister with a light, making her cry. He arrives at the museum, just in time to see Joshua attempt to push his sister in her carriage down a large flight of stairs, but he stops when he is caught by his grandmother, whom he proceeds to push down the large staircase, killing her and disguising it as an accident. However, Brad is convinced Joshua pushed her and confides in Ned at the funeral.

That night, Brad installs a lock on his bedroom door and tells Joshua that Lilly will be sleeping with him, fearing Joshua will attempt to do something to his sister. That night, Joshua builds a house of blocks in the living room and provokes his father. Brad tells him he won't be able to hurt anyone else, as he now realizes he is causing trouble. Later that week, on Ned's recommendation, Brad brings Betsy (Nancy Giles), a psychologist, into the home to meet Joshua. Betsy comes to the conclusion that Joshua is being abused. Later, Brad tells him he is being sent away to a boarding school, causing Joshua to run away. When Brad arrives home, he finds Joshua hiding in a cupboard, crying hysterically with a large bruise on his back.

The next morning, he and Joshua go for a walk with his sister, but Joshua has stolen her pacifier, causing her to cry. When Brad confronts him, he begins to mock him, causing Brad to strike him. After Brad realizes what he did, he tries to apologize. Joshua further taunts him, which drives Brad to beating his son in public, strengthening Joshua's case of abuse and sending Brad to jail for child abuse and assault. In addition, it is indicated that Joshua has framed his father for tampering with his mother's medications, suggesting that Brad will spend the rest of his life in prison, leaving Ned to adopt Joshua and his sister.

In the last scene of the film, Joshua is playing a piano while his uncle Ned is talking to a person in a phone about having a nanny to take care of Lilly. Afterwards, Ned sits with Joshua and the two compose a song with Joshua singing an original song. The lyrics of the song are basically how Joshua's parents both will never be loved by anyone due to all the events. It is then revealed in the song that he only wanted to be with Ned and got rid of everyone else.