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Kevin Parson is a 28-year-old seminary student at the Divinity School of the Pacific, South, in Long Beach, California. A late convert who found faith three years earlier, Kevin lives alone and keeps his troubled past hidden, including from Dr. John Francis, the dean of academic affairs. After a Friday discussion with Dr. Francis about the nature of evil, Kevin receives a call from an unknown man who identifies himself as Richard Slater. Slater claims to know Kevin intimately, gives him three minutes to confess his sin to a newspaper, poses a riddle, and threatens to blow up his car. Kevin panics, drives across traffic into a parking lot, and dives out moments before the car explodes.

Detective Paul Milton of the Long Beach Police takes charge, and forensic scientist Nancy Sterling determines the bomb used dynamite with a remote detonation mechanism. Milton presses Kevin for a motive, but Kevin withholds Slater's demand that he confess a sin, fearing police will uncover his past. Kevin's parents died when he was one, and his aunt Balinda Parson adopted and raised him on Baker Street. Returning home, Kevin finds that Slater has infiltrated his house, leaving a childhood hair ribbon and a cell phone. Slater calls with rules forbidding police involvement before deadlines and demanding obedience. He threatens to kill Kevin's childhood friend Samantha Sheer within thirty minutes.

Kevin calls Sam, who works for the California Bureau of Investigation (CBI) in Sacramento. Together they solve the riddle and realize Slater's target is Damon, Kevin's childhood dog, still chained at Balinda's house. Kevin races to Baker Street, where his family lives in a self-constructed alternate reality. Balinda, who insists on being called "Princess," and her husband Eugene maintain an elaborate fantasy, burning any books or newspapers deemed unreal. Their intellectually disabled adult son Bob greets Kevin joyfully. When the deadline passes, an explosion kills Damon. Kevin's childhood memories surface: At age ten, Sam appeared at his bedroom window and coaxed him outside through a window held shut by a single screw. She became his secret best friend, as Balinda forbade Kevin from going outside.

FBI Special Agent Jennifer Peters, a forensic psychologist, enters the case. She has spent a year tracking the Riddle Killer, a serial offender who murdered five people in Sacramento, including Jennifer's brother Roy Peters. She profiles Slater as intelligent and methodical, noting the car bomb had no termination switch, meaning Slater never intended to stop the detonation.

Saturday morning, Slater calls with a new riddle and a sixty-minute deadline. Sam arrives and Kevin confesses what he has never told anyone: As a child, he locked a threatening boy in an underground cellar and left him to die. At age eleven, a boy with a knife and a knife tattoo on his forehead stalked Sam and threatened to kill them both. Kevin trapped the boy in a warehouse basement, slamming a steel door and throwing the deadbolt, then returned months later to find bloodstains but no body. Jennifer arranges for the confession to air on live television. Sam deduces that Slater's target is a bus, and she and Kevin evacuate the Third Street bus. Slater accuses Kevin of breaking the no-police rule and detonates it.

Jennifer drives Kevin to Baker Street to jog his memory. He recalls the boy's knife tattoo, their first real identifier. Jennifer visits Balinda's house and discovers the extent of Kevin's abuse: Balinda isolated him, withheld food and water, forced him into cold bathtubs, and tried to suppress his intellect. Kevin sneaks away from Sam and buys a .38 revolver. Slater's next riddle leads them to a warehouse, where Kevin encounters Slater in the darkness and fires three shots before Slater escapes. Slater detonates the real target: the Augustine Memorial Library at Kevin's seminary. Kevin evacuates the building and barely escapes.

Kevin tells Jennifer about his childhood in full. Balinda adopted him at age one as a playmate for Bob and, when Kevin proved more intelligent, controlled every facet of his reality through isolation and deprivation. Kevin did not leave until age twenty-three. Before dawn Monday, Slater kidnaps Balinda and locks her in a hidden basement. Sam travels to Houston, where a witness's timeline proves Slater cannot be the Riddle Killer. Sam suspects Kevin and Slater may share the same body through Dissociative Identity Disorder, a condition in which distinct personalities inhabit one person. She realizes she never actually saw the threatening boy.

Sam sneaks into Kevin's house and finds notes for a seminary paper bearing the characters "| AM |" in Slater's handwriting, which she interprets as "I am I," and a second cell phone matching every call Slater made. Kevin receives Slater's demand to come alone and save Balinda. Armed with his revolver, he evades surveillance, reaches the toolshed in Balinda's backyard, and descends through a trapdoor into a bomb shelter. In the basement he finds Slater's lair and hears Balinda behind a steel door.

Slater emerges, a muscular blond man with a silver gun, and reveals his plan to frame Kevin by making the world believe Kevin has Dissociative Identity Disorder, using the planted phone and manipulated voice recordings. He forces Kevin to call Sam and lure her to their location. Jennifer and Dr. Francis, working in parallel, reach a different conclusion. Francis theorizes that Kevin, raised in Balinda's fabricated reality, created distinct personalities: Samantha to embody good, Slater to embody evil.

Sam traces Slater's riddle to the basement beneath Kevin's childhood window and enters through the toolshed tunnel. When Slater wounds Sam, Kevin bleeds from the same injuries. The FBI lab confirms both voice recordings belong to a single person. Jennifer and Francis realize the full truth: Slater is a personality of Kevin's, and so is Samantha. Kevin has three distinct personalities. Jennifer has never met Sam in person, and no one named Samantha Sheer was ever registered with the CBI.

Jennifer calls Sam and tells her she is one of Kevin's personalities. Inside the basement, Slater forces Kevin to hold a gun to Balinda's temple and another to his own head. Sam tells Kevin the truth: She and Slater are both parts of him. Shooting her would mean destroying the good in himself. Samantha steps forward, tells Kevin she loves him, and walks into his body, merging with him and disappearing.

Jennifer and Dr. Francis burst into the basement and find only Kevin, standing alone with both guns, bleeding. There is no Samantha, no Slater. Francis instructs Kevin to separate himself from Slater and shoot. Kevin points a weapon at the space where he sees Slater and pulls the trigger. The bullet buries itself in a metal desk. Slater vanishes. Kevin collapses in tears.

One week later, Kevin stands in Dr. Francis's garden, released on bail after Jennifer revealed his abusive childhood at a news conference. Kevin enacted all of Slater's and Sam's actions himself, from planting bombs to evacuating the bus, while believing he was his alter egos. Jennifer announces a sabbatical to oversee Kevin's therapy, and they acknowledge their feelings for each other. Francis reflects that Kevin's story embodies the struggle Saint Paul describes in Romans 7: The good one wants to do but cannot, and the evil one does not want to do but keeps doing, the three natures of man personified.