In Middletown, CT, musical prodigy Ben Stockton is in the car with his dad driving through the night in a storm. Ben is working on his music but his dad says he should try to do something else. Ben asks his father to slow down the tempo of the windshield wipers. Ben's father sees a woman pulled over to the side of the road and stops to help. He goes over to her car and calls a tow truck, but warns it's going to be a while. He offers to take a look at the car over her objections and sees a device flashing green/red lights. The frequency of flashing increases and he turns around to realize the storm has stopped and tow truck driver is there. The car has vanished and Ben is gone.
Broyles describes the case to the team and says it's happened before. There are three other missing-person cases dating back over three years, and each one involved the same woman. The victims were found later, driven insane. All of the victims were academics. Walter recognizes the green-red light sequence, but can't remember how he knows it.
Olivia and Peter talk to Ben's father and aunt, who explain that nine months ago Ben and his mother Abby were hit by a car. Abby died and after Ben emerged from a coma, he became a musical prodigy and continued working on the same piece of music.
The woman comes into the basement room where Ben is held and says there's someone who wants to see him. Ben insists he wants to see his father, but the woman notes that he may want to see his mother as well.
At the laboratory, Walter is working with flashing lights and attempting to remember where he knows the lights from. He admits he worked with an advertising firm to develop similar technology, and thinks the lights could be used to induce a hypnotic state. Walter demonstrates by having Peter stare at the flashing lights. Peter blacks out and discovers that time has passed and he's cut the sleeves off his shirt.
Charlie calls Olivia to inform her they've identified the kidnapper from the father's description as Joanna Ostler, a molecular biologist who died ten years ago. However, the body was never found. Olivia checks in at the lab and they compare notes, and Walter remembers that the man who mentioned the lights to him was Dashiell Kim, his roommate at the mental institute. It turns out Dashiell was abducted the same way and was locked up after he went insane and bludgeoned is wife to death. Broyles warns that Dashiell is flagged as knowing top secret government data and it'll take at least six weeks to get clearance.
Joanna takes Ben through the steam tunnels to a room with a piano and sheets of music taped to the wall. His mother Abby is there, her face scarred, and they hug.
Walter examines the photo of the murder scene when Dashiell killed his wife, and recognizes the formula written on the wall. Dashiell couldn't complete the equation and he tried to kill Walter when he helped. As they listen to the recording of Ben playing his music, Peter spots a recurring expression in the equation. They convert it into music… and it's the same song Ben is composing.
Ben wonders if they're in Heaven and doesn't understand how Abby can be there. She says it's important he finish his song and he agrees.
Olivia visits Dr. Sumner, the head of St. Claire's. He remembers her taking Walter out of the institute and insists Walter has no business being out in the real world. Olivia says that Walter is doing fine and has been helping the FBI in their investigations. Sumner doesn't want to have his patients interrogated by the FBI and refuses to give a new person access to Dashiell. When Olivia says that a child's life is in danger, he agrees to let Walter talk to Dashiell.
Olivia goes back to the lab to discuss the situation with Peter. Peter refuses to let Walter go but Walter insists on making his own decision. He admits he'd rather not go but he has no choice but to do so to save the boy. They go to St. Claire's and Sumner greets a nervous Walter and escorts him in to see Dashiell. Things go well at first but when Walter asks Dashiell about the woman who abducted him, Dashiell claims ignorance. Walter uses a marker to draw out the formula and tries to get Dashiell to remember. Dashiell insists he doesn't do math anymore and the other inmates panic. When the orderlies try to take Walter away, he lashes out at them and Sumner sedates him. Sumner refuses to release Walter as he may pose a danger to others. He's checked Walter's involvement with the FBI and warns that they've exacerbated his mental instability. Olivia threatens to get a court order but Sumner refuses to be intimidated.
Walter is locked in a cell and looks up to see someone come in: himself. H is duplicate sits on the bed and welcomes him back.
Charlie updates Olivia on their search for Ben when Olivia gets a call informing her that there are problems with getting Walter out. They have to wait until the morning to get the court order, and Olivia apologizes to Peter admitting he was right. Peter notes that Joanne was walking around she must have used an alias. He suggests that they run patterns based on "Ostler," which is Middle English for "innkeeper." He comes up with a match to a P.O. Box in Clarksburg, Maryland belonging to Joanne Ritz.
Ben is playing at the piano with his mother but he hesitates and she encourages him to continue. However, when he says he doesn't know how it ends, she starts bleeding from the cuts on her face. Joanne tells Ben that if he loses her again, he only has himself to blame.
Walter goes to see Dashiell and apologizes for upsetting him. Dashiell tells him to go away and Walter sees himself across the courtyard. Walter tells Dashiell about Ben and asks for a description of the woman. Dashiell finally says that Joanne promised him whatever he wanted, but when he couldn't solve the equation, she took it all away. He talks about how Joanne filled his mind with images of the people he loved and then ripped them apart to force him to do the work. It becomes clear Ostler is projecting images into her victims' minds. He says he was in a dungeon in a red castle, and Walter dismisses it as a fantasy. Dashiell collapses, sobbing, and says it was nothing but a bad dream.
Peter arrives to get Walter and accuses Dr. Sumner of doing something to harm Walter. Sumner wonders how Peter is now with Homeland Security and says that he's gone over Peter's history and he's not a fit guardian. Sumner plans to petition the state to have Peter removed as Walter's guardian. Peter warns Sumner he has no idea what he's capable of. Peter is escorted to see Walter, who says that it was all for nothing and wonders if that's what it's like when Walter talks to Peter.
Charlie and Olivia are checking the streets of Clarksburg when Peter calls Olivia, and mentions the red castle and dungeon that Dashiell described. As she hangs up, she sees a nearby red carousel that resembles a castle. They go inside and Olivia finds a ladder leading down into the team tunnels. They go down and Olivia finds a room with Ben strapped up to a device. Joanne attacks her and they struggle for Olivia's gun. Joanne gets down the tunnel and Olivia grabs the gun and tells her to stop, but Joanne activates the hypnotic light sequence and escapes when Olivia goes into a fugue state.
Peter and Walter return to their hotel room and Walter insists he needs space and wants his own room. Peter notes that Walter was brave for going back to St. Claire's.
Joanne meets with Mitchell Loeb and they take the equation and plug it into a laptop computer. They then attach the computer to a safe and put an apple inside. Loeb reaches through the side of the safe and removes the apple… and then shoots Joanne dead. He calls someone and informs them it worked.
Olivia looks on as Ben is reunited with his father.