Worcester, Mass. A sad-looking man, JOSEPH MEAGAR, is awakened by his shrewish mother. He's late for work because his clock-radio is on the fritz. He scribbles some numbers in a notebook, then takes his temperature. When his mother berates him for his irresponsibility, she suddenly grabs her heart -- her pacemaker is malfunctioning.
Joseph arrives at work, Bicoastal Parcel Service, and opens his locker to reveal an advertisement torn from a magazine and pasted in the locker door: "Unlock Your Hidden Potential." As Joseph gazes fondly at the picture of a girl captured on his cell phone camera, his jerk boss ridicules and criticizes him. Then Joseph's package scanner goes on the fritz and starts smoking, meaning he'll have to record deliveries by hand.
Joseph makes a delivery to an office in downtown Boston. And who is the receptionist but BETHANY, the very same girl we saw on Joseph's cell phone. Joseph makes awkward small talk, until they are interrupted by Bethany's suave and confident co-worker. They're going out for drinks later. While Joseph absorbs that blow, Bethany freaks out as her computer crashes.
Joseph enters the building elevator, followed by Bethany on her way to fetch an IT person. Joseph drops his phone, and she sees her picture on it. She is creeped-out, and Joseph tries to explain himself -- but then the elevator car takes a sudden jolt. A momentary pause... and then the elevator plummets downward, accelerating, slamming into the ground floor in a spectacular crash. Bloody and broken bodies cover the floor. But Joseph, seemingly unharmed, gets up and sees the dead Bethany. Joseph exits through the parking lot, and all the cars' ignitions turn over, sirens blaring as he runs from the building in terror.
Olivia and Charlie are walking down the street, and Olivia is clearly not herself. Finally, Olivia confesses that she saw John Scott -- her dead partner and former lover -- in her kitchen the previous night. She imagined it, of course, but it bothers her. Charlie says it's okay; this kind of reaction to trauma is to be expected.
In the lab, Broyles tells the team about a mysterious power surge in downtown Boston that caused an elevator to literally drive itself into the ground. A similar event caused a Mag-Lev train in Tokyo to plow through the wall of a train station. These events may be harbingers of a new weapon technology.
At the elevator crash site, a technician explains that the elevator's motor drove the car right through the safety brakes -- almost as though another generator had come online. Walter, inspecting the bodies, says the passengers were electrocuted. They were all dead by the time they hit the ground! Walter takes Olivia's necklace and lets it float in the center of the elevator car, thus demonstrating that the whole area is still charged with magnetic energy.
Back in the lab, Walter discusses a Cold-War era project to make people trackable by homing pigeons. Humans are actually highly complex electrical systems, and each person possesses a unique electromagnetic signature that, in a theory, a pigeon could follow. But the human electromagnetic field was too weak to detect, so they tried to amplify it. The unfortunate result was damage to nearby electrical systems. As Walter explains this, a human heart from one of the elevator victims lying on the table unexpectedly beats. Someone has amplified a person's electromagnetic field, Walter says, and that's what is powering this heart. A person was the source of the accident.
Meanwhile, Joseph returns to Bicoastal Parcel, where his boss rebukes him and then fires him. Joseph pleads for another chance, but is interrupted when the boss's arm gets trapped and mangled in a package-sorting machine.
Olivia is working late when Broyles comes in. Upon hearing Walter's theory that an altered person may be controlling electrical devices, Broyles tells Olivia about a cluster of off-the-grid medical clinics that collect clients using bogus claims on TV -- weight loss plans and so forth -- and then experiment on the subjects. Broyles says a man named JACOB FISCHER is behind a number of these clinics, and he's wanted for illegal human alteration. This suggests that if someone is controlling electricity, maybe someone else made them that way.
Later. Olivia's work is interrupted by the lights going out. Olivia goes into the hallway with a flashlight. The elevator rings, and to Olivia's shock, John Scott appears. He says he's here to help her. She's on the right track looking for a person, but Fischer is after him, too. She has to reach the guy before Fischer does. Reacting to Olivia's accusations of betrayal, John says that one day he'll prove he really loved her, always. But until then, she'll just have to wait. Then the elevator doors close. Olivia runs down to lower level to catch the elevator opening. But when the doors open, John is gone. And at the rear of the elevator car, Olivia sees the weight capacity sign: "Maximum capacity: 2000 pounds."
Peter and Walter's hotel room. Olivia reveals her discovery: the weight sensor in the elevator showed a total weight, before the crash, of 165 pounds more than the total weight of the victims. Someone must have walked out alive! But why didn't he get electrocuted and crushed like everyone else? Walter posits that the survivor must have been the source of the electromagnetic energy, and a form of electrodynamic levitation allowed him to escape the brunt of the impact. The senselessness of wrecking an elevator on which you are a passenger leads to the conclusion that the effect may have been unintentional. This man may not be in control of his powers, which means the team should be looking for small electrical anomalies.
At the FBI, Charlie documents a variety of electrical anomalies in downtown Boston, from malfunctioning automatic gates to CCTV cameras.
Joseph arrives at home and tells his mother he thinks he made a mistake. He read an advertisement in a magazine promising to unlock his hidden potential. He went to an office, where they said they could realign the electrical impulses of brain to mimic those of a more confident person. His mother denounces him for a fool, and as Joseph becomes increasingly upset, his mother's pacemaker goes haywire and kills her. A shocked Joseph packs his bags to leave -- but on his way out he is intercepted by Fischer, who shoots him with a tranquilizer.
Charlie gets a report on a man who lost a hand in a conveyor malfunction at Bicoastal Parcel. He links this to the building's visitor log, where Joseph Meagar had signed in to make a delivery for Bicoastal Parcel. Olivia goes to Joseph's apartment and finds the dead mother.
Back in the lab, Walter finds the Walkman that Joseph left behind in the elevator. He says the cassette tape inside was magnetized by Joseph's unique electromagnetic signature. Walter isolates the signature and says they can use it to find Joseph. How? With birds!
In an undisclosed location, Joseph is strapped to a surgical bed with electrodes implanted in his temples, pleading with his captors to be released.
Back in the lab, the team has brought in cages full of homing pigeons. Walter places them in a cylinder situated between Tesla coils. He activates the coils, surrounding the birds with electrical current to reorient their magnetic sense to seek out Joseph's unique signature.
Olivia is in the hallway again, getting a soft drink, when John reappears. He kisses her and says he didn't betray her. "I wasn't the one." Then Peter arrives, and in the blink of an eye, John vanishes. Apparently Peter could not see him.
In Harvard Yard, the team prepares to release the birds. With a wild thrumming and fluttering, the pigeons take flight. Astrid and Walter track the birds using GPS transponders strapped their feet, while Peter and Olivia follow them by car.
At the secret clinic, Fischer performs a painful procedure on Joseph. "You don't realize what you are," Fischer tells him. "Look what science has made you: special."
Now the birds have stopped, circling over a building. The team arrives, and Olivia and Charlie enter with guns drawn. Inside, Joseph's abductors put him in the back seat of a car and prepare to escape. Joseph uses his power to accelerate the car forward, smashing a thug against a fence. Meanwhile, Olivia confronts Fischer. Charlie handcuffs him while Olivia goes after Joseph. In a mad chase through a factory yard, Joseph powers up heavy machinery and blows out power lines to stop her. But he doesn't anticipate Peter stepping out from behind a bus and knocking him out with a crowbar.
A heavily sedated Joseph is rolled out on a gurney, headed for the hospital. He tells Olivia that he just wants to go home, that he never wanted to hurt anyone. Olivia regretfully says they can't let him go home. He has to be examined.
Back at the lab, Walter shocks Olivia by asking if she's been seeing John. He's not surprised to hear that she has. There is a reason, he says. These are not mere hallucinations. When Olivia and John's minds were linked (see episode 1), part of John's consciousness and memories crossed over into her mind. Olivia says that John appears in the flesh and talks to her, and Walter says that's because he doesn't belong there. There is only room for one consciousness in Olivia's brain, so her mind is expelling John's. Will he go away? Walter says doesn't know, and pointedly asks: would she want him to?
Olivia is driving her car somewhere in Boston when she sees John walking along the sidewalk. She jumps from her car and follows him down to a cellar. John seemingly entered without problem, but Olivia has to shoot the lock to enter. Inside she discovers a room filled with files.
Later, at the FBI, Broyles explains that John Scott must have been doing his own investigations. There is no sign of who he was working with. Many of the files are encrypted and could take months to translate. But John definitely knew about the Pattern, and he knew more about Fischer. Fischer is refusing to cooperate with the authorities, but John's files have allowed them to locate some other test subjects like Joseph. Also, Broyles says, they found John Scott's personal effects, and some were seemingly intended for her. Inside a box, Olivia finds photographs... and an engagement ring. Olivia remembers what John told her: "You know I loved you... always." And then she sees the word inscribed on the ring: "always."