At the BAU, JJ asks Hotch where Elle is. Hotch tells her Elle went to Dallas to do a custodial interview with William DeVries, the child murderer, for the VICAP program. JJ is surprised that such a new BAU member would be given such a big responsibility. Hotch expresses his confidence in Elle's abilities.
On a train going through Texas, we get a glimpse of people in one of the cars. The camera pans past a middle-aged man (Ted Bryer) sitting alone, then focuses on a college-aged guy (Josh) listening to his iPod. He is remembering running his car into a building because he had been drinking. He had called his dad to tell him about it and his dad got very angry and told him not to bother coming home. Further along the train, a pretty twenty-something woman (Elaine) sits down by herself and looks out the window. She is remembering a positive pregnancy test, and how her boyfriend told her they could get married. She didn't want to get married, and told him she was "going to Dallas to take care of it." She is very sad.
In another seat on the train a businessman sits. He (Harold) seems nervous, wiping his sweaty brow with a handkerchief before looking at a gun he has concealed in his briefcase. He is remembering packing the gun after his wife told him she was leaving him. She insists she is going to Dallas and doesn't want him to follow her. A few rows away, a professional woman is reading the paper. She (Linda) is distracted by the memory of someone asking her if it is a good idea to "take him" to Dallas. She remembers answering that she had written two books "on this" already and that he proved her theories. They were both going to that conference in Dallas.
A few rows away, Elle sits, looking at a case file full of pictures of young boys and bloody crime scenes. She pulls out her cell phone and calls Gideon. In Gideon's office, his desk is overrun with files and papers. She tells him she wants to go over the file again before her interview so she decided to take the train. When he tries to give her advice she sarcastically calls him "Dad." Gideon is trying to put her off because he is extremely busy, and the cell phone connection is not very good. He hurriedly says they can talk tomorrow, and the cell connection is broken. During the conversation, we see a figure we hadn't noticed before seated behind Ted Bryer, the middle-aged man. This figure is watching Elle. He leans forward to speak to Ted and points out that Elle is reading an FBI file. Ted asks him to leave him alone, but the strange man, Leo, is whispering in his ear. Ted looks directly across the aisle at the professional woman and her newspaper. The words on the newspaper seem to move and change as he looks to read "We See You." Leo, still whispering, says "I told you where we were really going."
Suddenly, the train jerks to a stop. Everyone is startled, but a train security officer comes through the car and advises everyone to be calm, everything is fine. When he notices that Elle is holding an FBI file he leans down to tell her someone jumped onto the tracks to commit suicide and that it happens so often they have a protocol to follow.
Leo whispers that this is Ted's opportunity, points out the officer's gun, and encourages him to do something. Ted is very upset, grabs the officer's gun and shoots him twice in the stomach. Leo shouts "Get the agent!" and Ted smacks Elle across the face with the gun and takes her gun before threatening the rest of the people on the train. Elle tries to calm him and Linda asks him what he is doing. Leo tells him he has done a good job.
Back at the BAU, the team is slowly congregating in the conference room. JJ is showing a video of the inside of the train car, telling them there are five hostages, one security guard dead from initial gunfire, and the train stopped on the tracks. What they are seeing is from a security camera on the train, and it is live. The BAU has been called in because of a particular psychological angle, and Reid immediately notices that the hostage taker, Ted Bryer, is showing signs of Tardive Dyskinesia – severe facial tics that are the sign of years of taking anti-psychotic medication. JJ summarizes the case, saying there is a psychotic on a train in Texas with hostages and two guns. Gideon enters, and hears about a hostage situation on a train in Texas. He peers at the screen and is appalled to realize Elle is one of the hostages.
The BAU arrives in West Texas, driving a black SUV. Morgan, Hotch, Gideon, Reid and JJ talk about the situation as they drive in. Both SWAT and HRT teams had already arrived at the area and positioned themselves around the train car. A mobile command center had been set up. Morgan calls Garcia to have her work facial recognition software to find out who the other hostages are. Morgan is very professional with her, calling her "Penelope", and telling her that Elle is one of the hostages. Garcia's usually playful manner is immediately reined in and she advises him she is "into it."
It took two hours to set up a mobile phone, and still the hostage taker won't speak with anyone but the "Higher Authority." The unsub won't speak to the lead crisis negotiator, only giving him three hours to produce this authority 2-1/2 hours ago. Gideon advises Hotch to put on the lights and sirens and to arrive at the scene with lots of fanfare. They will pull up as close as possible, and then wait 30 seconds before exiting the vehicle. They aren't to look at the train. Gideon says this is the way the "Higher Authority" would act.
Inside the train, the mood is extremely tense - Elle has been handcuffed to her seat. Leo and Ted watch the FBI arrive out the window. Linda asks Ted to listen to her, but Ted responds angrily, pointing the gun at her. Josh tells her "your boyfriend is whacked out of his mind." Linda tells him Ted isn't her boyfriend, and Elle realizes that he is a psych patient. Linda identifies herself as his doctor, and that she was taking him to Dallas because of his improvements. Ted is anxious, sometimes squeezing his eyes shut as if in pain. Linda advises that they try to make Ted feel less threatened, even though he is the one who is threatening the hostages. Elaine is sick, and Linda realizes that she is pregnant.
Linda rises and calmly approaches Ted. Leo advises him that this is a trick and Ted yells at her to sit down. Harold slowly opens his briefcase, and before anyone can react, he pulls out - a Bible.
Ted is more and more anxious as he watches the motionless FBI vehicle out the window. Josh is drinking and making sarcastic comments.
The team meets with Frank Morreti of the Dallas Field Office, and advises that the only demand the hostage taker has is to talk with the Higher Authority. Hotch moves away to talk with the HRT commander – the head of the SWAT team. Gideon tells Morreti they have to find out the level of the unsub's delusions. Reid goes through a list of possible psychoses, and begins to talk in detail about the popular movie about John Nash, who heard alien voices, before he's stopped by Morgan.
The HRT commander tells Hotch they are in position. Hotch advises that even though they may be able to talk their way out of it, there may be a point when they must rush the train. HRT advises they are ready when needed.
On the train, Ted tells the hostages that "This is going to end today."
In the mobile command center, the team wonders what Ted believes is happening here. Gideon is trying to figure out what a Higher Authority would do, and decides he would wait for Ted to come to him. Ted pulls the pregnant girl up by her hair and drags her to the front of the car by the phone even as Elle tries to convince him to take her instead. Leo advises Ted to not let Elle talk to the other agents. Josh tries to intervene, and Ted hits him. By the phone he tells the pregnant girl not to say anything he hasn't told her to, not to send them any "codes". She is confused but plays along. He has her call and ask Gideon who he is. Gideon acts as the Higher Authority, being very mysterious and cryptic. Ted is confused and upset, and Gideon tells Ted to ask his own questions. Letting Elaine go, Ted tells Gideon he "wants it removed now." Gideon tries to put him off, threatens to hang up, before Ted gives him one hour to "remove it or, I swear to God I'll kill every agent on this train."
Morreti asks Gideon, "Do you know what IT is?" Gideon replies he doesn't, but they have an hour to figure it out. Reid advises that while some delusions are more common than others, delusions are varied and colored by personal experience.
Leo tells Ted he can't turn back; his paranoid comments keep Ted agitated. Linda tries to help Josh with the cut on his head. Elle asks about cell phone reception, but no one has any. Elle then tells Linda they need to know what IT is. She tells the hostages that Ted thinks the government is watching and monitoring him. Josh seems on board with the "conspiracy theory" that the government watches everything. Ted is distracted by Josh's comments and threatens him until Linda calms him, holding his right arm up to show many small scars, and telling him "they want to divert you from having IT removed."
Inside the field office, Gideon notices the attention on Ted's arm – scars – Ted's concern to have it removed has to do with a microchip. Reid agrees, this is a common delusion. Ralph Tortorici took a oom hostage believing the government was controlling him through a chip in his body. Garcia calls Morgan with the names of the people on the train – she identifies everyone including the hostage taker: Dr. Theodore Bryer.
Gideon and Morgan go through the hostages, watching their info appear on a computer screen. Harold takes no chances, Josh is a drunk and reckless, Elaine lives off the grid, Dr. Linda Deaton is a psychiatrist for Ted Bryer and a popular lecturer. The team feels none of these people will help, and they might hurt, the situation.
Inside the train, Leo advises Ted that the people outside are "messing" with him, that he needs resolve. As the hostages talk together, Linda tells them Ted thinks everyone on the train is a government agent. Josh stands up and tries to make friends, but his attempt to get on Ted's side doesn't calm Ted down, but only aggravates him more. Leo tells Ted the hostage is trying to use Ted, is laughing at him. Linda calms Ted once more.
The BAU team is desperately trying to come up with a scheme to remove a chip that isn't there. Since Ted is lucid and relatively aware of his surroundings, they won't be able to trick him easily, and since he's convinced the chip is in his arm which he can see, not the back of his neck, it won't be easy to fool him. Reid comes up with the idea of using sleight-of-hand - a magic trick he's been practicing all his life. He hides the chip in his palm and then "takes it out" of Ted's arm. Hotch and Morgan are against it, but Reid shows them, with a coin, how he can make it appear and disappear. Hotch doesn't want to give Ted another agent as hostage, and Morgan tells Reid to teach the trick to him. Reid can't – he's been doing it his whole life - he can't teach it to him in 30 minutes. Although they don't want Reid on the train with an "armed psychotic", Gideon realizes they have no other choice.
JJ and Gideon discuss Ted Bryer's background – his government research on string theory and M-theory – his brilliance and his institutionalization for nine years.
Linda tries to talk to Ted again. She tells him he is in no danger. As she talks, Leo argues against every word she says. Linda offers to stay if he lets the rest of the hostages go. Seeing her through Ted's eyes, she turns into robed angel in white, threatening to kill him. He moves to shoot her, and Elle intervenes, telling him if he shoots anyone else, she will make sure "they never take it out of you; they will leave it in you forever." Seeing the stress on the train, Gideon calls to ask if everything is all right. Ted insists they take it out, he will only allow one technician, and he wants it done now.
Hotch removes a small chip from his phone for Reid. As Gideon looks on, Morgan dresses Reid in a flak vest – telling him not to take it off. He reviews SWAT tactics reminding Reid that he might not have any advanced warning of their plans. Morgan tells Reid not to make eye contact with Elle, but to "play into the guy's fantasy." Reid does it a little too well, and makes Morgan smile.
Outside, wearing latex gloves, Reid has trouble doing the trick with such a small chip. He practices, dropping it again and again until he gets it right. The team is extremely tense, giving Reid advice, telling him to immediately get off the train once he's done. Reid asks for a favor before he leaves: "Could at least one of you look like you're going to see me again?"
The walk to the train seems long for Reid behind the police lines and barricades. The team watches anxiously as he approaches the train car and Hotch advises HRT to get whatever targets they can, as it might go bad fast. Ted is holding Elaine in front of him as Reid enters. Leo issues orders to Ted which he immediately obeys. Ted tells Reid to take the vest off. Reid tries to argue, but Ted has a gun on Elaine and insists. Inside the mobile office, Morgan and the team are worried.
Reid sits across from Ted, who lets Elaine go. As Reid nervously works on Ted's arm, the hostages watch, fascinated. When he cuts him and pulls the chip out "of his arm," the hostages are amazed, but Ted is happy that he was right. As Reid rises to leave, Ted points his gun at Reid's chest and tells him to "turn it on."
Hotch, Gideon and Morgan are anxiously waiting for Reid to get off the train. The HRT commander tells Hotch it will take at least two shots to bring Ted down – one to shoot out the window and one to shoot him. Hotch knows Ted will begin shooting hostages when he hears the first shot.
Elle helps Reid, by saying the chip has to be implanted to be turned on. Reid tries to leave again, but Ted won't let him. Gideon calls and Reid advises Ted to answer the phone, that he must answer to the "Higher Authority" for not following directions. Leo tells Ted not to listen, but Ted is tired of people telling him what to do, and wants everyone to "leave me alone." Josh angrily interjects that this was the government's fault, talking about tracking and monitoring devices. Elle, Reid and Linda try to get Josh to sit down, Leo argues, and Ted is completely agitated. He aims to shoot Josh, but Linda steps in front of Josh and takes the bullet.
Ted finally answers the phone, telling Gideon he's tired of fighting. He tells Gideon, "It all ends today." The BAU team knows this means Ted is going to kill himself and all the hostages. Elle tries to talk to Ted, but Leo tells him not to listen. Reid asks Ted to get Linda help by talking to the Higher Authority. Ted's response is to shoot the phone. Hotch goes out to get the HRT team ready to go in.
Ted begins talking to Leo, telling him that he can still hear the chip, still feel the buzzing and burning. Reid, watching him, realizes that Ted is talking to someone only he can see – Leo is not there, has never been there – he's only real for Ted. Reid stands up and gets Ted's full attention. Ted threatens him with the gun, but Reid is calm, talking about Leo as if he can see him and hear him, too. He tells Ted he knows what it's like to hear voices. Reid even talks to Leo, asking him to leave Ted alone. Ted seems to be responding, as Reid tells him he understands, that the voices helped him learn and come up with his string and M-theories, theories that no one else had ever developed. Ted can see the strings that make up the universe, even those that make up Reid's body.
The BAU team is worried that all of Ted's attention now seems so focused on Reid. Ted approaches him until he is standing right in front of Reid, next to Elle. Gideon is afraid for him, afraid he'll push Ted too far, and gets ready to go into the train himself. But Ted is really listening to Reid, he may be willing to give up, he tells Leo to shut up. As Ted turns to speak to Leo, Elle grabs the gun out of Ted's waist, and Reid grabs the hand holding the other gun and struggles with him.
Outside the train, Gideon hears one shot go off. We can see in his face that he is afraid Ted has shot Reid or Elle. He races towards the door. Inside the train, Reid is still holding onto Ted, but the gunshot came from Harold. He has shot Ted in the chest. Reid also takes his gun and tells Gideon they need an ambulance.
Later, outside the train, Morgan stands over Ted who is strapped into an ambulance gurney, whispering the words "I'm sorry," over and over again. Morgan responds, "It's a little late for that," before moving off to ride in another ambulance with Linda, who will also live.
Elle and Reid are sitting on the back bumper of a police car, where Elle complains to Gideon about being required to go to the hospital. When he asks if she's all right, she responds, "I'm fine, Dad." He tells her never to call him that again, and walks off. She wonders to Reid if he'd prefer "mom." Cringing, Reid advises against it, but doesn't mind rubbing in that he saved her life and it was all "caught on tape." She asks him about his words to Ted about understanding what it was like to hear voices. He denies any underlying meaning, telling her he was trying to gain Ted's trust, and it worked. Reid tells her to go to the hospital, he'll see her there, and walks off.
As Reid and Elle walk away, Reid's voice is heard: "Albert Einstein asked the question that sometimes drives me hazy: am I or the others crazy?"