Children gather at Frank's house to help celebrate Jordan's birthday. As Jordan blows out the candles, Frank experiences a series of internal visions, including one in which he is trapped underwater, gasping for air. Moments later, a deliveryman brings a package to the house. Inside are Polaroid photographs.
FBI agents gather inside the conference room to hear about the case. Among them is Special Agent Del Boxer, who listens with suspicion as Frank recounts his past experiences with receiving Polaroid photographs. He tells the group that the technique was the M.O. of a killer who is now dead. Three years earlier, he began receiving the photos yet again, but the sender is believed to be deceased as well. In the past, the photos have been of his family. This time, he is the subject of the photographer's lens. Boxer points out that the stills, which depict a drowned Frank floating in a body of water, have all been doctored with the aid of a computer. He also believes that Frank knows more than he is revealing.
Frank tells Emma that he is hiding something from his fellow agents. He describes how, as children, he and his brothers went swimming with some friends. One of the friends played a trick on Frank by yanking him under the water. One of Frank's brothers retaliated by doing the same to one of the boys. Unfortunately, the boy didn't resurface. The boy's body was eventually dragged onto shore, but firemen were unable to revive him. Frank has never been able to put the incident out of his mind. That night, Frank experiences a nightmare in which the stalker attacks him with a knife. When Frank awakens, he moves towards Jordan's bedroom to see if she is all right. Suddenly, an intruder appears. Using a Polaroid camera, the man blinds Frank with a flash. Frank then tumbles down the stairs.
Frank places Jordan in the care of her grandparents until the intruder is apprehended. However, he is unable to provide investigators a description of the intruder. This, coupled with a lack of physical evidence, leads Boxer to conclude that Frank concocted the entire story, perhaps as part of a nervous breakdown.
Frank pays Father Yahger a visit at St. Timothy's. Yahger is familiar with Catherine through her dealings with the church. Frank tells the priest he feels the presence of evil. Frank confirms that he has reconciled Catherine's passing. But when Yahger asks him if he has reconciled his own, Frank is again struck by the internal images. Frank is left speechless, as the thought had never occurred to him.
When Frank returns to his office, a mail clerk hands him an envelope. Frank immediately instructs everyone, with the exception of the clerk, to evacuate the building. He explains that anyone who came in contact with the envelope may have been exposed to a mass contagion. The incident turns out to be a false alarm, as the envelope contains a piece of mail that had been forwarded from Frank's old address. A short time later, Frank announces that he is leaving the FBI.
Frank realizes that someone has had access to his therapist's files. He pays the therapist a visit, and tells her that for the first time, he is experiencing how a victim feels instead of how a killer thinks. The therapist encourages Frank to seek out those he trusts - and to let them help. Frank takes the therapist's advice and telephones Emma, who is at St. Timothy's church. Frank makes arrangements to meet Emma there. Meanwhile, Agent Boxer pays Frank's therapist a visit. Boxer states that the therapist's science and understanding are powerless against Frank's fear. He then produces one of Frank's kitchen knives and raises it into the air. Moments later, Boxer morphs into Mabius.
When Emma emerges from the church, she sees a form off in the distance, standing in a graveyard, someone who resembles Frank. The figure suddenly runs off, and Emma gives chase. The figure disappears, and as Emma looks about, she sees a freshly-dug grave. Someone suddenly pushes her forward, and she topples into the hole, landing in a casket. When Frank arrives at the church, he experiences an internal vision, and sees Emmas being buried alive. He instructs the priest to call paramedics to the scene. Frank and his fellow agents pull an unconscious Emma from the casket. Emma eventually regains consciousness. McClaren and Boxer question Frank about how he knew of Emma's dilemma. Frank cannot explain how he knew. And when Frank's therapist turns up dead, Frank can only assure the pair that he is not the killer.
Emma telephones Frank about the incident at the graveyard. Frank still cannot explain how he knew of her whereabouts. Moments later, Frank hears someone inside the house. Frank follows the killer, who disappears into the bathroom. The room, however, turns out to be empty. Suddenly, the bathroom door swings shut, and Frank finds himself trapped inside. The faucets begin gushing water, and the room begins to flood. Emma enters Frank's home, where she comes upon an identical version of herself. The second Emma points a gun at herself and fires, committing suicide. The bathroom door strains and creaks from the pressure of the building water. It gives way, saving Frank at the last moment. Frank opens his eyes, as if reborn. Moments later, he realizes that everything - the bathroom, the floor, and his clothes - are dry. Emma, meanwhile, discovers that her second self has vanished. Frank finds Emma and holds her.