A young executive, MARK YOUNG, arrives late to give a presentation. After he has finished and the boardroom empties, Young collects his things, and then spots a butterfly. It alights on his finger -- and unexpected cuts him! The insect flutters by his neck -- and cuts him again. After attacking him a few more times, the creature disappears into AC vent. Young peers into the vent just as a SWARM of butterflies pours out. As they surround him, cutting him all over his body, he runs in mad panic. He crashes through the plate glass window and falls to his death. And now the location is finally revealed: Massive Dynamic's New York office.
Boston. Olivia Dunham is getting ready for a night out, but before she can leave she is summoned by Phillip Broyles to catch a plane to New York. At the scene of the apparent suicide, Walter Bishop notices lacerations beneath Mark Young's shirt, even though there aren't corresponding tears in the shirt itself. Meanwhile, Olivia spies John Scott -- her dead partner and lover -- in the crowd of onlookers. He stares at her for a moment, then vanishes.
Olivia meets with Nina Sharp, COO of Massive Dynamic. Nina suggests that Mark Young must have succumbed to the stresses of his job, as some small fraction of employees always do. When Olivia presses for more, Nina says that, given Olivia's recent work, she should understand how the discovery of certain unexpected realities could be too much for some to handle.
In Young's apartment, Olivia and Charlie find a plane ticket that implies Mark Young was not planning to kill himself. In Young's day planner, Olivia finds a page that has "MONARCH" written on it. On the wall nearby, she sees a display of captured butterflies -- whose wings unexpectedly start to flutter. Charlie causes Olivia to turn away, and when she looks back the wings have stopped fluttering.
The laboratory. Walter, examining Young's body, notes that his wounds go clear to the bone, as if they had started inside and opened upward toward the surface. Also, Young had some kind of synthetic compound in his brain, but that wouldn't explain his wounds. Meanwhile, Peter receives a call from a WOMAN -- someone from his past who wants to see him.
In her apartment, Olivia studies the Massive Dynamic website. She performs a web search for resources on "monarch," finding only pages on English royalty and butterflies. After she shuts down the laptop, it mysteriously starts up on its own, and an email pops up -- from John Scott! It contains only an address: 1312 Labrador Lane, basement level.
Moments later, Olivia arrives at the address. As she walks through the darkened basement, she hears strange croaking noises. Finally she finds a room filled with giant plastic tubs. She opens one to see that it's filled with toads.
FBI office. Charlie asks Olivia why she just charged ten pounds of live insect larva to the Young investigation. Olivia admits to Charlie that she's still seeing visions of John Scott, and she feels like she's going crazy. She wants to take a personal leave to get her wits together. Then Astrid calls with news: Walter thinks Young's death was because of the toads!
In a diner, Peter meets with TESS, the woman who called earlier. There is clearly a history between them. She pleads with him to leave Boston: "If I can find you, they can find you." Peter takes her hand -- and notices the bruises on her wrist. He infers that someone named MICHAEL did this, and Tess doesn't deny it.
Back in the lab, Walter explains the principle of psychophysiologic effects: the ability of the mind to produce physical effects in the body. He shows old video footage of an experiment he did many years ago, in which a hypnotized man believed an ice cube was burning him -- and produced real blisters. But how does this relate to the toads? Walter says these particular toads, bufo alvarius, secrete a psychoactive compound from their skin. Properly modified, the compound is a powerful hallucinogen. The modified version of it directly affects the fear center of the brain. Walter suggests this was murder, as the concentrations of the compound in his brain were ridiculously high. Young was literally scared to death! He imagined the cuts, and his brain made them real.
Olivia admits to Walter how she found the toads: John Scott led her to them. Walter suggests that a form of repressed memory therapy could be used to raise the memories and purge them from her head. But doing so would pose serious risks to Olivia's health. Despite the warning, Olivia insists on getting back in tank, as it could provide the key to cracking the Mark Young case.
As Olivia prepares for the procedure, Walter explains how it will work. The first time she connected in this manner with John Scott ("Pilot"), some of his memories crossed over into her brain. This time, they will attempt to bring those repressed alien memories to the surface. Walter's voice will be Olivia's tether to reality.
In a dream state, Olivia spots a door and walks through into a restaurant -- the same place she and John Scott went on their first date. And in fact, it is their first date! Olivia watches a slightly younger version of herself sitting in a booth with John Scott.
The younger Olivia stands up and walks past her. Because this is only a memory, Walter says, no one cannot see her. Nevertheless, Olivia sits down in front of John. He's indifferent, clearly unaware of her presence. She tells him that she loved him and trusted him. Still no reaction. But when she changes direction and says that Mark Young killed himself yesterday, suddenly John Scott looks her right in the eye. "He sees me!"
The scene abruptly changes. Now Olivia is in John Scott's car, alone. Walter says John must be there somewhere. Olivia exits the car and finds a meeting of four men: John Scott, Mark Young, and two unknown men -- one black, one Latino. Young walks away with the Latino. Olivia follows, but as she turns a corner the two men suddenly vanish. Walter says that's because she's seeing John's memory, and John didn't follow them. Olivia returns in time to see John brutally stabbing the black man to death. She screams to be pulled out of the tank.
Outside the tank, Olivia and Astrid use the computer to reconstruct the face of the Latino man she saw in John's memory. Olivia tells Broyles they think Young was killed for selling the synthetic compound to black market buyers. In the wrong hands, it could be turned into a cheap street drug or even a chemical weapon. Olivia wants MD to release information on all of Mark Young's projects.
A street in South Boston. Peter stops a man on the street and gives him a serious beating. Pointing a gun at his face, Peter says, "If you touch her again, I'll kill you." Apparently, this guy must be MICHAEL.
FBI office. They've had no luck with face recognition software. Broyles provides Olivia with a file of all Young's projects, courtesy of Nina Sharp. Inside, she finds Young's business card, with the phone number 877-8MSS-DYN at the bottom. That gives her an idea. She dials 212-MON-ARCH on her phone, and someone answers. Olivia pretends to be telemarketer, and the person on the other end says to take his number off their list. Olivia recognizes that voice! It was the Latino man in John's memory.
The number is traced to a man named George Morales, a known black market trafficker. Olivia and Charlie follow his cell phone signal through the streets of Manhattan. When they hit a traffic jam, Charlie and Olivia close in on foot. Morales jumps from his cab and runs, but he is hit by an oncoming car, allowing Charlie and Olivia to apprehend him.
In the hospital, Morales says he wants to make a deal. He will tell them everything, in return for protection -- from Massive Dynamic. He believes the firm killed Young as a warning to anyone else who might try to sell the company's secrets. He denies having killed Young himself, because he had no reason to do so; Young was a valuable source of amazing technologies. Moreover, Morales says the Pattern is just a hoax, a smokescreen created by Massive Dynamic to enable them to do anything they want. Morales believes he can trust Olivia because John Scott told him about her.
Massive Dynamic. Nina says that the firm has nothing to hide. And she's not surprised at all that Morales, a criminal, spun an outrageous story in which Massive Dynamic is responsible for all his foul deeds. Olivia tells Nina that now is the time for her to come clean, before Morales spills everything he knows. Nina expresses doubt as to whether Morales will say anything actionable.
Meanwhile, John Scott enters Morales' hospital room. Morales, clearly frightened, promises that he won't tell anyone anything, but John Scott slits his throat anyway. A nurse walks in to see Morales' throat slitting itself, opening from the inside out. Somehow, Morales must have been dosed with the same drug that killed Young.
When Broyles tells Olivia the news, Olivia blames Nina Sharp. But Broyles says Massive Dynamic has been nothing but cooperative, so she should keep her unfounded accusations to herself.
Olivia tells Walter she wants to go back in the tank one more time. Walter refuses. Every time she goes in, the chances of a catastrophic outcome increase. And she might not even get what she wants from John Scott, because she can't just ask him. When Olivia objects that John Scott actually saw her in the dreamscape, Walter says that's simply impossible, because only his memories are in her head. But he leaves her with a promise to try and find a safer way to retrieve John's memories.
In an undisclosed location, Michael -- stilled bruised from Peter's beating -- tells an unidentified man that Peter Bishop is back in town.
Olivia, in her apartment, receives another mysterious email from John Scott: "I saw you in the restaurant."