Middletown, Conn. JEREMY STOCKTON drives his car through stormy weather, while his son BEN sits in the back, writing musical notation. He asks his father if he can slow down the windshield wipers, because the tempo distracts him. Jeremy pulls over to assist a YOUNG WOMAN on the side of the road, who is apparently having car trouble. He calls for road assistance, then offers to take a look at her engine. Under the hood, he sees a mysterious pair of lights flashing -- green, green, green, red... green, green, green, red. He is seemingly transfixed until...
He's startled by the tow truck driver tapping on his shoulder. The rain has stopped. The young woman has disappeared. So has her car. And to Jeremy Stockton's dismay, so has his son.
Boston FBI office. Phillip Broyles describes the abduction to Olivia Dunham. This is not the first abduction of this kind; three other people have been abducted by a woman meeting the same description. The previous abductees eventually turned up, physically unharmed but mentally insane, unable to remember what happened to them. Olivia observes that all the previous abductees were academics and experts in their fields, and Ben doesn't fit this pattern. Walter Bishop, who has been listening in, says something about lights: green and red, like Christmas lights. He's heard this story before, but he can't recall where or when.
Olivia meets with Jeremy and his sister. Hearing that the previous abductees were experts in various fields, Jeremy tells an unusual story about his son. Ben and his mother Abby were in a car accident, and Ben's mother was killed. Ben was in a coma for six days, and when he awoke, he suddenly had the ability to play the piano -- despite not having had a single lesson. Soon he was composing his own music, and he had become obsessed with one particular composition.
In an undisclosed location, Ben sits in what looks like a basement. The young woman who abducted him says there's someone who wants to see him: his mother.
The Harvard laboratory. Walter is singing Christmas carols in an attempt to jog his memory about where he heard the story of the lights. He still can't remember, but he does recall an experiment he did for an advertising agency that involved flashing lights to induce a form of mind control. The experiment failed. But Walter thinks flashing lights might have been used to put Jeremy in a hypnogogic trance while his son was abducted. Walter believes his previous experimentation failed because he studied only the speed and intensity of the lights, not their color. He asks Peter to looks at some lights. Peter stares as they flash... green, green, green, red... but concludes that it's not working. Then he realizes that his sleeves have been cut off. He asks Walter if he did this, and Walter replies, "You did."
Meanwhile, Charlie Francis has identified the kidnapper from a sketch based on Jeremy's description. Her name is JOANNE OSTLER. She supposedly died ten years ago, eight months before the first abduction. But her body was never found.
Back in the lab, Walter has finally realized where he heard the story about the lights. Lights lead to Christmas, Christmas leads to the lyric "dashing through the snow," and that leads to Dash. DASHIELL KIM, a fellow inmate from the asylum! Dashiell told Walter a story about being hypnotized by a Christmas tree.
Olivia briefs Broyles on Dashiell Kim, an astrophysicist who vanished for a week, then had a psychotic break when he returned. He bludgeoned wife to death with a tire iron. Olivia wants to visit him at St. Claire's mental hospital. But Broyles says he's classified as criminally insane with knowledge of state secrets (because he had a sideline consulting on defense contracts). That makes access extremely limited, and it could take weeks to get it.
The woman, whom we now know as Joanne Ostler, shows Ben his pages of sheet music arranged in a way he's never seen before. Then, to Ben's surprise, his mother ABBY appears. He runs to her and they embrace.
At the lab, Olivia shows Peter the crime scene photo of Dashiell's home, where he killed his wife. Mathematical notations have been scrawled all over the wall. Walter recognizes the notations as an equation that Dashiell was obsessed with but could never solve. Peter notices a recurring mathematical expression on the wall, and he suggests this could be a rhythm. He asks Walter to translate the math into standard musical notation. While Walter works, Peter explains that music is really just a mathematical language, where chords and notes have numerical equivalents. Walter finishes his translation, and Peter plays it on the piano. It sounds very much like Ben's composition. Walter realizes that Ben's piece is the musical equivalent of Dashiell's equation. But what are they both trying to solve?
Ben is still with his mother. A healed scar is visible on the side of her head. She says that in order for her to stay, Ben has to finish his composition. So Ben starts to play.
St. Claire's Asylum. Olivia meets with Dr. Sumner, the director of the institution, to request a meeting with Dashiell Kim. Sumner realizes that Walter Bishop is the reason she wants to meet with Dashiell, and he offers his opinion that Walter has no business being out of the institution. He also refuses to allow Dashiell to be subjected to open-ended interrogations by people he's never met. But he suggests a compromise: Walter can come back long enough to talk to Dashiell.
Olivia and Peter argue about whether to allow Walter to go back to the asylum. Peter is vehemently opposed. But Walter interjects, and reluctantly volunteers to go because a boy's life depends on it.
Inside, Walter talks to Dashiell, who denies knowing any story about a woman hypnotizing him with lights. Walter continues to press Dashiell for answers, causing him to become increasingly agitated. When Dashiell tries to leave, Walter tries to stop him, the two men wrestle, and Sumner steps in and sedates Walter.
Against Olivia and Peter's wishes, Sumner insists on holding Walter overnight. He says Walter's work with Homeland Security has exacerbated his worst delusions. Olivia will need a court order to override Sumner's decision.
Walter lies in his old cell, fitful and unable to sleep. Then someone arrives and sits down on the bed. "Welcome back, Walter." Walter looks up to see that his visitor... is a cleaner, healthier version of himself.
FBI office. Olivia is told by the general counsel that they can't get the court order to release Walter until morning. Peter asks Olivia if they've tried to find an alias for Joanne Ostler, which of course they have -- unsuccessfully. Peter says that he whenever he used an alias, he would pick something close to the truth, like substituting King or Knight for Bishop. A quick computer search reveals that Ostler is Middle English for innkeeper, which gives Peter the idea of hotel names. He discovers that a "Joanne Ritz" has a P.O. Box in Clarksburg.
Ben can't seem to finish his composition. His mother sweetly encourages him. But when he still fails, the scar on his mother's head starts to split open, oozing drops of blood onto the piano keys. Ostler tells Ben that if he loses his mother again, he'll only have himself to blame.
In the morning, Walter meets with Dashiell again. As Walter looks through the bars, he sees the other Walter again, across the yard, watching him. Walter presses Dashiell for information about where his abductor took him. Dashiell begins to cry. The woman promised him beautiful things, but then she took them away when he couldn't solve the equation. She hurt him and put him in a dungeon, where she tried to suck the answers from his head. As Dashiell says these words, we see where Ben really is: strapped to a chair in a basement, with wires coming from his head while Ostler takes notes. But when Walter presses Dashiell for a location, all he can remember is a red castle.
When Peter arrives to take Walter home, Sumner threatens to have Peter's guardianship revoked. Peter talks with Walter, who is disappointed in himself. All Dashiell could do was rave like a loon. "Is that what it's like to talk to me?" Walter asks Peter.
Clarksburg, Mass. Olivia and Charlie have been canvassing house to house. Peter calls and tells her that Walter couldn't get anything from Dashiell, just incoherent stuff about red castles and dungeons. Olivia turns around to see, just past the trees nearby, a red brick building with a tower on top.
Olivia and Charlie enter the warehouse, where Olivia finds a basement entrance. They split up downstairs. Olivia finds Ben strapped to a chair. But before she can free him, Ostler attacks her from behind and a fight ensues. Ostler runs and Olivia gives chase. Ostler pushes a button on a handheld device. Olivia sees lights flashing in front of her... green, green, green, red... and is startled when Charlie taps her on the back. Ostler is gone.
Peter and Walter return to their hotel, where Walter announces his desire to have a place of his own. Peter promises to look into campus housing, and then congratulates Walter for being brave enough to return to St. Claire's.
In an undisclosed location, Ostler meets with MITCHELL LOEB (an FBI mole introduced in "In Which We Meet Mr. Jones"). She gives him the solved equation from Ben's composition. Loeb types the equation into a computer, and then attaches a strange apparatus to a locked safe. Wearing a thick rubber glove, he apparently reaches through the back of the safe to remove an apple that was inside. Just as Ostler expresses her astonishment, Loeb shoots and kills her. Then he makes a telephone call: "It worked."
At the FBI office, Olivia watches as Ben and his father have a tearful reunion.