In Queens, New York, the police close in on a parking garage. Two men hold a hostage, a 15-year-old boy. The police order the two men to get out and they cautiously emerge. One man warns the police that they have no idea what they're dealing with. The other man stares at the officer in charge, Gibson, and he backs away and drops his gun. He backs over the edge and falls to his death. Another cop, Officer Williams, shoots the two remaining officers and then puts the gun to her head and kills herself.
The Fringe team is called in to investigate and Broyles informs them that they're running photo recognition on the footage from the security cameras to identify the two men. The kidnap victim is Tyler Olson, who disappeared 36 hours ago. Walter is bored at the lack of cadavers and says he already knows what happened: the victims were influenced by mind control. Peter doesn't believe it, and notes that Tyler's father works for the aerospace division of Massive Dynamic.
Olivia, Walter, and Peter go to Massive Dynamic to meet with Nina Sharp and Dr. Carson. Walter is impressed by the entire facility, including its huge number of laboratories. Olivia asks Carson why he didn't call the police sooner, and he explains that he and Tyler don't talk much and he didn't know the boy was missing until the kidnappers called. Nina confirms that the two kidnappers, identified as Tom Dobbins and Patrick Hickey, and have no involvement with any of their clients. According to the police files, they're used cars salesmen. Nina and Olivia assume that the men are trying to extort secrets from Massive Dynamic, military software for government aircraft. When Dr. Carson admits he doesn't know what he would do if he lost his son, an upset Walter walks out. Peter goes after him and Walter admits that he's envious of how much William Bell has achieved. Walter notes that Bell introduced him to Peter's mother, and it was her idea that Walter and Bell would form a company together. Fortunately, she was there for Peter while he was gone.
Tyler gets hungry and Hickey and Dobbins stop at a store and Hickey demands all the money. When a customer tries to interfere, Hickey mentally controls him into pouring hot coffee onto his head, shattering the jar over his head, and running into a glass case. The clerk draws a gun and tells Dobbins to get out, and Dobbins controls him into putting the gun down and sticking his car keys into an electrical outlet.
The team arrives to investigate the crime scene, and Peter notes that the kidnappers don't seem to have a plan. They wonder why Tyler didn't run and why the kidnappers didn't simply take the money. Broyles calls to confirm that Hickey and Dobbins were seemingly ordinary car salesman, albeit the best at their dealership. Both men had perfect records and simply took a loaner car and disappeared. Peter and Olivia speculate that their foreign intelligence agents who blended in by taking ordinary jobs.
At the lab, Walter opens up the dead officer's skull to check for lesions on the brain caused by the mind control. He shows Olivia and Peter hematomas indicating trauma: the result of mind control rather than simply hypnosis. Walter believes it's transmitted through sound waves, and Olivia asks him to find a way to block it so they can get to the men.
Broyles is with Dr. Carson with the father gets a call from Tyler. They listen in as Tyler his father to give them what they want. The men demand $2 million and specify a drop-off time and place. They're unable to get a trace. Olivia wonders why the men simply want money and suspects that it's a distraction so they can get something else. She suggests they set a trap.
At the lab, Walter goes through his old equipment after muttering something about Peter's childhood. He finds an old teddy bear and explains that it generates white noise to simulate the womb, and they can use it to block the agents' mind control.
Olivia explains to the FBI team that they want the kidnappers alive and turns the meeting over to Walter. He explains that they've been given audio-adapting earphones that will give off white noise to block the mind control. Each team leader will have a microphone that lets them communicate with their individual team members.
The FBI teams surround the drop site and Dobbins drives in. Hickey approaches on foot. Walter activates the white noise generator but there's no sign of Tyler. Hickey grabs the money and tries to run, and Dobbins drives out through a door as a diversion. Olivia goes after them but Peter spots Hickey and goes after him on his own.
Olivia finds Hickey, begging for help and trying to kill himself with an empty gun. Meanwhile, Peter suddenly comes to a halt and removes the headphones. Tyler is standing there with the money, and tells him that they don't work. He then commands Peter to take him to his car and they drive away.
Afterward, Olivia has her people try to find Tyler and Walter informs her that Peter has disappeared. Hickey explains that he and Dobbins were the hostages and Tyler controlled them into doing what the boy wanted.
As Peter drives, he gets increasing head pains and Tyler says he can make it stop as long as Peter does what he says of his own volition. When Peter tries to pull over, Tyler takes control and forces him to speed up until Peter agrees to obey him.
Olivia tells Nina what they've learned and demands to know what the connection is to Massive Dynamic. Nina notes that Carson works in aerospace, but he's been collaborating with their pharmaceutical division on one project. They go to the flight simulation deck and Nina explains that the system is a hands-free process that monitors the pilot's thought waves. The pilot is given a drug to enhance their brainwaves. Nina insists that Massive Dynamic doesn't allow family members as test subjects, but Dr. Carson admits that he took some samples home.
Peter tries to get answers from Tyler about the limits of his powers, and points out that the boy really hasn't thought anything out. He figures that Tyler has a vendetta against his father and admits that he has the same problems.
Dr. Carson insists that the drug wouldn't let his son control human brains, but Walter points out that an adolescent boy could prove receptive to the drug's influence. He confirms that Tyler was taking psychostimulants for ADD, and condemns Dr. Carson as a poor parent who has endangered Walter's son.
The police come up behind Peter and Tyler, and the boy refuses to accept Peter's advice to give it up. Tyler has Peter pull over and tells him to take care of it, or he will. The officer orders Peter out but Tyler forces him to give the gun to Peter. He then controls Peter and starts to make him shoot the officer. Peter begs him to stop and Tyler finally has Peter knock the officer unconscious.
As Olivia and Astrid coordinate the manhunt for Tyler and Peter, Olivia is summoned to Nina's office. Broyles informs her that Tyler has been tagged a national security threat and the Fringe Division has been ordered to stand down. They've learned that Tyler bought two one-way tickets to Costa Rica, before he abducted Peter, and they believe that he's working with a foreign power to deliver secrets. Overwhelming force has been authorized and Olivia worries that Peter will be harmed. Broyles says they have to contain the situation themselves before it's too late.
Olivia and Nina check on Walter, who insists that he can't lose Peter again. Olivia tries to reassure him and says they need him to find a way to neutralize Tyler's power. Walter is totally confused with Peter at his side but Olivia assures him he can do it. Nina steps in and tells Walter that he's the only one that can help, no matter how scared he is. Walter considers using an EMF scrambler to disrupt Tyler's mental transmissions. Astrid comes in to inform them that she' checked Tyler's computer and he's been doing net searches on women in their mid 20s who died in car accidents 14 years ago. They determine that the last woman he checked on was Renee Davies. Olivia takes the information to Dr. Carson, who admits that Renee is his ex-wife, Tyler's mother.
Peter convinces Tyler to go to a strip bar. He questions the deaths that Tyler has caused and the boy insists that murder wasn't part of the plan: they just got in the way. When Peter admits he can understand Tyler's father issues, Tyler says that he's not done yet. The teenager explains that his father lied to him and said his mother was dead.
Dr. Carson explains to Olivia that Renee was taking drugs and disappeared for weeks at a time when Tyler was a baby. She finally disappeared for good, and Dr. Carson never told Tyler since he assumed Renee would die of an overdose somewhere. Finally he told Tyler that she died in a car wreck, so he wouldn't know his mother abandoned him.
Tyler tells Peter that he finally found his birth certificate and learned his mother's name, and discovered she wasn't dead. Now she's a rehab councilor and Tyler plans to reunite his family. When Peter objects, Tyler takes control of him again and has him drive a knife into the seat, and then warns him it would have been his leg if he didn't need him to drive. He then tells Peter that they're going.
Walter has rigged a tin-foil hat, but to protect his thoughts from Massive Dynamic. He's learned that the pilots exposed to the drug were susceptible to magnetic fields so he's modifying an EMP pulse to target Tyler's thoughts and wipe his thoughts long enough for them to take him down. They pack it up and head for Renee's rehab home.
In Springfield, Renee is working in her garden when Tyler and Peter arrive. Tyler introduces himself as her son and embraces her, and Peter suggests they go inside. Tyler explains that he blames his father for her leaving and Renee tells him that wasn't the case. Her new husband Seth comes in and Peter tries to get Tyler out, but the teenager reasserts control on Peter and has him take out the policeman's gun and aim it at Seth.
Broyles and Olivia arrive and Broyles goes in the front while Olivia takes the back. They realize that Peter is going to shoot Seth and Broyles goes in to stall for time so Walter can set up his equipment. He tasers Tyler but the boy retains control of Peter and has him shoot Broyles in the arm. Tyler leaves with Peter as Olivia comes in seconds later. Broyles tells her to go after Tyler and she gets into the car with Walter and Astrid and they follow Tyler.
The team quickly spots Walter's stolen car and Walter warns that they need to get within 20' feet for the EMF generator to work, and it will only last for a few seconds. Astrid closes in and Walter activates the device, and Tyler blanks out for the few seconds necessary for Peter to drive into a telephone pole.
Peter wakes up to find Walter hovering over him. His father compliments him on his quick thinking. Tyler received a concussion in the crash and they're giving him a sedative to keep him unconscious. Broyles is okay and assures Peter that he's okay, and Peter explains he managed to pull his aim off-center.
That night, Olivia calls Peter, and he tells Walter that he was correct and Tyler's power disappeared once the drug wore off. Tyler will be going into therapy. Walter offers to make him crepes and Peter assures his father that he's okay. Walter talks of how Peter used to call them "creeps" when his mother made them, and talks of how she was a strong woman.
Nina writes a letter to Bell in the other reality, hoping he'll receive it along with the others. She tells him that the Penrose-Carson project has resulted in one Tyler with mind-control powers, but he sought out his surrogate mother. The other Tylers were placed with other Massive Dynamic scientists. Nina suspends the experiment indefinitely. As Dr. Carson wheels the unconscious Tyler into a ward filled with other unconscious Tylers, Nina concedes that despite the grisly results, the experiment was a success.