In Middleton, Connecticut its pouring down rain, a man is driving with his son in the backseat. They get flagged down by a woman who claims that her car is having problems. The man calls a tow truck and offers to look under the hood for her. When he opens the hood he is bombarded by red and green flashes, he is startled out of his hypnotic state when the tow truck man taps on his shoulder.  The man turns around to find that the woman, her car and his son are missing.

Agent Broyles debriefs Olivia and Peter on the missing boy situation at FBI headquarters. He states that the father claims that even though he never lost consciousness he did lose time. He then goes on to inform them that this is not the first time this kind of situation has happened. There are three other cases dating back ten years in which witnesses describe seeing the same woman. The FBI has put their description of the woman through facial recognition software but nothing comes up. The victims were let go but they did not come back the same, they came back insane. For example a woman tried to lobotomize herself using a butter knife and none of them could recall what had happened to them even under hypnosis. Olivia discovers that each of the victims were academics except Ben who is a ten year old child.

Walter surprises Agent Broyle by stating that there was also peculiar flashing Christmas lights.Walter can't remember how he knows it.

Olivia goes to visit the Mr.Stockton, Ben's father at his home. He claims that he isn't crazy and Olivia comforts him by saying she believes him. She then explains to him that they think this has happened before but Ben doesn't fit the profile of the victims. That's when Mr.Stockton tells Olivia that nine months ago Ben and his mother were hit by a car while crossing the street. His mother died but Ben was in a coma for six days. When he came home, before even saying a word he went straight to the piano and started to play. Mr. Stockton shows Olivia a DVD of Ben playing a piece of complex music and startles her by saying that Ben had never onc taken a piano lesson. He then goes on to state that in two weeks time Ben was composing his own music, one piece in particular that Ben obsessed over because he couldn't finish it. Ben's aunt believes that maybe this is what Ben expertise was and this could be the reason why he was kidnapped.

Ben is being held in a dimly lit basement, the woman who kidnapped him enters to asks how he is doing and he only answers by asking to go home.She then tells him that his mother would like to see him.

Back at Harvard Walter is singing Christmas songs and playing with Christmas colored lights in order to re jog his memory.He does recall that in a previous employment that lights were used to sway shoppers, even though that didn't work he does know how to do it now. He uses Peter to test his theory of the lights being the key ingredient. Peter doesn't believe it works until he realizes that his sleeves are cut off his shirt and he is the one that did it.

Charlie finds out the identity of the woman who has been doing the kidnappings. Her name is Joanne Ostler, a neurologist studying at MIT, who died ten years ago.Her car went over a bridge eight months before the kidnappings even started, the  car was recovered but the body never was.

Walter in the midst of singing Jingle Bells realizes that he heard the story of flashing lights from Dashel Kim, a fellow inmate at St.Claire's Asylum. He was the head of Astro physicis at UMass, went missing in 2006, turned up a week later at his home where he had a psychoti break killing his wife with a tire iron. The team encounters a problem in seeing Kim when its discovered that he is a 1027, a criminal that knows state secrets.

Ben led by Joanne is brought to a room where he finds a piano, his music and his mother.She persuades him to finish the song because she can only stay with him if he finishes it.

Olivia shows Walter a picture of the Kim murder scene but instead of the body he sees the equation that Kim was obsessed with written on the wall. Peter realizes that the equation that Kim was obsessed over is the same as the music that Ben obsessed over, the math translated into music is the the same as Ben's song.

The head of St.Claire's Asylum, Doctor Sumner, refuses to let Olivia see Dashel Kim. He will only let Walter come into the Asylum to ask Kim questions. Peter is against it but Walter states that he would rather not but he will do it for the child. Peter and Olivia accompany Walter to the Asylum assuring him that they will be there when he comes back. Walter finds Kim and asks him out right about the Christmas lights, Kim claims he has no idea what he is talking about. Walter writes the equation for him and Kim convulses into a fit sending the room into chaos. The orderlies seize Walter and sedate him. Sumner claims that Walter is in no state to be released, that his state of mind is being affected by the work he is doing for the FBI. Olivia threatens to get a court order and Sumner tells her to go right ahead because he's not releasing Walter.

Peter and Olivia can't get Walter out until the morning. So they work on finding out the identity of the woman. Peter figures out that her name means innkeeper and if she used a derivation it would align with hotels which leads him to a p.o box for Joanne Ritz.

Ben is having trouble figuring out the last part of the song and as a way to keep him working Joanne starts to make the scars on his mothers face start to bleed.

Walter finds Kim in the asylum and gets Kim to explain his abduction, as he relays his experience we are given flashes of Ben tied to a chair with a helmet of wires attached to his head. Ben is not really in a room in a piano with his mother, Joanne is feeding him those images through a computer to get him to finish the song. Kim tells Walter that he was in the dungeon of a red castle.

Peter is able to get Walter out of the Asylum with a slip from Homeland Security. Walter tells Peter about Kim's red castle and dungeon and only when he relays that information to Olivia that they make a break in finding Ben.
Olivia finds a red amusement building that resembles a castle, she enters it with Charlie having her back. They split up and she finds Ben attached to a metal chair his mind hooked up to a computer. Joanne attacks her from the back and they get into a fight. Joanne escapes by unleashing the red and green flashing lights on Olivia. She is startled when Charlie puts his hand on her shoulder, revealing to the both of them that Joanne had indeed escaped.

Joanne drives to a warehouse where she meets a man who types the finished equation into a machine that is hooked up to a steel box. He places an apple insid the box closes the door and puts rubber drape on the front of the steel door. He then puts on a rubber glove and as the machine makes the steel box vibrate he puts his gloved hand through the steel box pulling out the apple, without ever opening the box. Once they both realize that the experiment actually worked the man kills Joanne. Then he calls someone letting them know that the experiment worked.

Ben is reunited with his father.

I will never be able to look at Christmas lights in the same way ever again. What did that apple easily going through a steel door have to do with anything? Will there be perhaps be an episode in which people will be going through portals. Other than that question this episode really got back to the heart of the matter the father - son relationship. Walter is faced with his insane self in his time at the Asylum but it looks as if instead of taking him back a little closer to crazy it has propelled him to be a little more responsible. Will Walter start to have conversations that actually make sense? Say it ain't so because who else will provide a little comic relief