Kelly and Pax watch over Meadow, and Kelly worries that Glen somehow frightened Andy based on the boy's reaction. Once Meadow takes Andy to school, Kelly has to admit that there's nothing going on. Once she and her partner leave, Billy finds Meadow, who welcomes him with open arms. He takes her to a van and takes her into the back, and then he asks if Kelly is ready. Meadow says that sister soon will be and Billy says that his life without Kelly adds up to nothing. He then gives Meadow a trigger device and opens a curtain, revealing a man bound and gagged. He's rigged with jumper cables, and Billy tells her to enjoy. Meadow hits the button, shocking the man over and over again. Billy finally tells her to stop... for now.
Jeff and Skye watch the episode and Jeff points out that Billy is growing progressively more insane. Skye points out that they're approaching the season finale while looking up the term "neural fusion" that Phillip mentioned on his tape. She gets three hits on article abstracts published by Dr. Robert Kimble thirty years ago. They check the Internet and discover that Kimble is a professor of cognitive science at UCLA.
Nate is in a hidden chamber watching episodes of Cult and scribbling down notes about everything that he sees and hears. Stuart and Cameron watch him from an observation booth and Cameron worries that Nate may not succeed. He complains about all of the blood that they've spilled, including that of their own, and worries that Stuart has been wrong about the answers hidden in the show. Stuart reminds his fellow Moon Hill survivor that they have no idea what happened to Phillip and his followers, their parents. He's given his life to find them, compromising his daughter Kirstie, and warns Cameron never to question him again.
When Jeff and Skye track down Kimble at UCLA, they find his TA Allegra Constantine giving a lecture in his place. They approach her afterward and ask where Kimble. Allegra claims that Kimble is out sick and refuses to give them the professor's home phone number. When Skye wonders why she's acting suspicious, she explains that they're looking into Kimble's article about neural fusion. As they enter Kimble's office, they discover that someone has searched the place, scattering papers everywhere. Jeff and Skye figure that the True Believers found another copy of Phillip's tape and learned about Kimble's theories. As they look around, they discover that Kimble had taken screen captures from Cult and pinned them to the walls, and they figure that Kimble knows about the show. They warn Allegra that her boss may be in danger, and she admits that Kimble went missing shortly after Cult premiered.
At the studio, Marti approaches Roger, who snaps at her. The actress comments on Kirstie, noting that the crew have realized that she isn't visiting the set anymore. Roger insists that it's none of their business and yells at everyone before walking off the set.
Allegra has no idea why Kimble was so worried about Cult, and Skye warns her that some of the show's fans are obsessed with the program. Jeff finds the drawer that held Kimble's notes on neural fusion and Allegra tells them that she had also done work on the theory, and that her name was on the notes. Skye and Jeff insist that she has to leave before the True Believers come back for her and the TA leaves with them.
Kirstie pulls up at the studio and Roger comes out to confront her. He demands to know why she was at Stuart's house, swimming in his pool, and she finally admits that Stuart is her father. Roger realizes that they've been conspiring against him and flies into a rage, smashing the car that Stuart gave her. He then tells Kirstie that he doesn't want to see either one of them and storms off.
Skye and Jeff take Allegra to Jeff's house for safekeeping. She tells them that thirty years ago Kimble developed a theory that television broadcasting was creating a state of shared consciousness. Over the years television has become ever more pervasive as everyone shares experiences by watching them on television. Viewers became ever more obsessed with their favorite shows, and Kimble believed that there was more to the shared consciousness than they could understand. As Skye and Jeff wonder how Phillip knew about Kimble's theories thirty years ago when he made the recording, Allegra starts rearranging the newer photos on the wall. She points out that the ones Nate had posted were in the same pattern. They figure that Allegra may understand the code and show her Phillip's book, and she notices it has a three-line symbol on the cover just like the book that Kimble had. However, she doesn't recognize the code and suggests that they tell Kimble. Much to Jeff and Skye's surprise, Allegra reveals that she knows where he is and calls him.
Kelly attends therapy with Meadow and sees her therapist, Dr. Marie Beaumont. Meadow is dealing with her memories about the night that home intruders killer their parents, and Dr. Beaumont asks if Kelly is willing to help. Kelly assures her that she'll do what it takes to help her sister.
Allegra takes Jeff and Skye to a meeting spot in the woods and Kimble arrives. He holds them at gunpoint and they show him the book and explain that it belonged to Phillip. Kimble knows Phillip and the church, and Allegra tells her mentor that intruders searched their lab. The professor puts his gun away and asks why they're involved, and Jeff explains that the True Believers abducted his brother.
Nate continues to scrutinize the episodes of Cult, furiously taking notes.
Kimble explains that Steven Rae wrote a professor into the first episode of Cult... and had Billy kill the character off. The professor believed that it was a death threat from Phillip and went into hiding. He knew Phillip from thirty years ago when Phillip sought out and befriended him. Phillip believed that television was a malevolent force, but he took Kimble's theory of neural fusion and twisted them to fit his own obsession.
Nate tells Stuart that he doesn't yet know what happened to the Moon Hill parents.
After Phillip took Kimble's theory, he found like-minded individuals and moved up into the mountains to start his cult. Kimble continued to visit him, trying to convince Phillip that he was wrong, but Phillip refused to accept that he was wrong. The professor finally gave up and all but forgot Phillip. However, when he saw the first episode of Cult, he figured that Phillip hadn't forgotten him and wanted him dead. Jeff warns Kimble that though Phillip has disappeared, his son Stuart is carrying on his legacy.
Stuart tells Nate that he has funded their organization and anticipated every possibility. However, Nate warns him that there is always some hidden factor. Stuart tells him to find the hidden factor and warns that Jeff's life depends on it.
Kimble remembers that Phillip used to fence with his son, and that the Phillip family in Europe manufactured knives and cutlery. Satisfied for the moment, Jeff and Skye take Allegra back to LA. She insists that they should call the police. However, as they arrive at her apartment, they discover that the police are already there. Someone broke into her apartment and attacked her roommate Nancy, and they spot True Believer Dustin in the crowd. Realizing the True Believers are onto Allegra, Jeff keeps on driving.
Kelly remembers a man with a birthmark on his face breaking into their childhood home and killing their parents while they hid under the bed. She has spent all of the years since trying to forget, and doesn't know what she would do if she met the killer again. Beaumont asks Meadow what she would do. Remembering how she tortured the man in the van, Meadow claims that she would forgive her parents' killers.
Kirstie meets her father and admits that Roger found out about how they were connected. She accepts the blame and Stuart is furious that their plan to use Roger to get to Steven is ruined. Kirstie offers to fix it but Stuart angrily tells her to stay way from Roger.
Jeff takes Allegra to his home and she confirms that Nancy was okay. The roommate says that she came home and the robbers attacked her. Allegra goes into the next room to get some sleep while Skye checks Phillip's history on the Internet. She finds a reference to the Reynolds family and they realize that the company logo looks like the three-sword brand that the True Believers use. There is a company photo of Stuart and they realize that he was the True Believer at the church as well as the teenager in the video of the Leland murder. When they check Stuart's financial records, they discover that he's recently opened a film development company next to the Cult studio.
Kelly is trying to sleep but has nightmares of her parents being killed, and then sees the killer in her room. She runs to the door only to find Billy waiting for her, and jerks awake. Meadow comes to comfort her sister and assure her that no one is there, and apologizes for making her relive their parents' murder. She tells Kelly that the two of them will be strong together and Kelly asks Meadow to stay with her throughout the night. As Meadow lies down, she smiles in satisfaction at the success of Billy's plan.
Jeff and Skye break into Stuart's production office and look around. They finally locate a room filled with security monitors and realize that he's been monitoring the Cult studio all along to get inside information. As they leave, Stuart arrives and spots them. He glowers at them but lets them pass, and they quickly take the elevator down and drive off. They go to Jeff's house, worried that Stuart may have sent someone there. When they arrive, they spot the flashlight of someone moving inside. Dustin steps into the street and shoots at them, and they quickly drive away. Skye and Jeff figure that something has changed and that Stuart no longer needs them alive.
Kirstie goes to Roger's manor and begs through the door, asking for forgiveness. She promises to do anything to prove her love, and Roger asks how he can ever trust her. Kirstie finally tells him that she's there without her father's permission, and hints that he would kill her if he knew. She says that her life is in Roger's hands now and he opens the door and promises that he won't let Stuart hurt her.
As Nate watches the Cult episodes in the hidden chamber, Stuart tells Cameron that they no longer need to blackmail Nate with Jeff's safety. Nate is now so obsessed with the show that he will continue seeking the answers on his own. Stuart then enters the chamber and gives Nate Phillip's book that they recovered from Jeff's apartment. He has worked out that Nate led Jeff to the book, and tells him that their deal has changed. There is now no escape for either Jeff or Nate, and throws the book at Nate.
Jeff and Skye get a motel room using cash and Skye wonders how they can go back to their normal lives. They discuss what they'd be doing if they weren't on the run, and they hear a car backfire outside. They go to the window to check it out and Skye wonders if they'll ever be okay again. Jeff assures her that they'll take the fight to Stuart and they hold hands.