In Springfield, Massachusetts, Greg Wiles is talking to a friend on the phone. After he hangs up, he gets a popup on his computer saying "What's That Noise?" He clicks on it and stares intensely at the screen, ignoring his mother when she comes in to say she's going out. Liquid starts to leak from Greg's eyes and he hallucinates a hand reaching out from the screen and grabbing his head.
Olivia and her niece Ella are playing a game when Rachel comes in to note that Ella hasn't brushed her teeth yet and lied about it. As Ella goes back to brush, Rachel talks about how her daughter reminders her of Olivia.
At the lab, Walter is talking about Darwin while Peter finds a letter addressed to his father. He throws it in the trash as Astrid gets a call from Olivia saying she's sending over a body. As Peter and Walter leave, Astrid takes the letter out of the trash.
Charlie and Ella talk to Greg's parents and they say Greg was a perfect teenager with no problems. They note he was on the computer a lot and give Olivia the name of his primary friend, Luke Dempsey. Olivia returns to the lab where Walter explains Greg's brain was entirely liquefied. She has Astrid check Walter's computers only to discover the hard drive has been fried. While she tries to retrieve the data, Olivia goes to a garage to talk to Luke Dempsey at his place of employment. Luke admits he was talking with Greg the previous night but had no idea how or why he died. The two of them know each other because their fathers worked together.
Peter calls Olivia to inform her they've found a new victim dead the same way. They meet Broyles at a car dealership where they find the corpse of the general manager, Anton, with his brains liquefied. Olivia talks to the salesman, who says they went to a strip club the previous night and Anton returned to the dealership afterward. The man has no idea who might hate Anton.
Back at the lab, Olivia reveals that the manager's computer was damaged the same way that Greg's was. Both computers downloaded a huge file before they crashed, but they have no idea where it came from. The phone on the wall rings and Peter answers it, but claims it's a wrong number. Peter says he knows a friend who can salvage the data. Once he's gone, Astrid says she knows who called and gives Olivia the letter Peter discarded.
Peter goes to see his friend Akim and offers him a rare gold coin that he won in a wager with the man. Akim agrees to check the hard drive and identify the program.
At FBI Headquarters, Sanford Harris approaches Olivia and asks what she's looking for in the new investigation. Harris thinks it's a waste of time for the FBI and believes it's a CDC issue. She shows him the photos of the victims and he says it's another excuse to support their autonomous Fringe Division. He tells her that he's going to remedy the situation and he gives her 12 hours to solve the case or he'll reassign it.
Akim tracks the downloaded program and discovers that it was sent from multiple locations across the Internet. However, he can determine it's downloading to an address right now: Olivia's home. Peter calls Olivia and they both drive to her apartment.
At Olivia's apartment, Rachel makes supper while Ella turns on her computer and activates a Paint program. Rachel's phone is turned off and she doesn't hear Olivia calling her. The same "What's That Noise" popup appears on the computer and Ella clicks on it. The images start to display and Ella sees the image of a hand reaching for her. Olivia races in, surprising Rachel, and discovers that Ella is in a trance but seemingly unharmed. After a few seconds, Ella comes out of her trance.
Olivia calls Charlie in and tells him what happened. He calls in computer forensics while Peter entertains Ella and Rachel congratulates him on being good with kids, and notes she's more the party type than Olivia. Ella says that she saw a hand coming out of the computer and Rachel doesn't believe her, but Peter and Olivia ask for more detail. Olivia examines the computer and notices that the camera is turned on. She's unaware that a man in a computer workshop at the other end is watching her. He says to himself that he's the one he's looking for. The man gets a security alert and his son comes in: Luke Dempsey. The man, Brian thanks his son for bringing lunch. Luke is concerned about his father, wondering if he found a job. He says that his father hasn't been home for a week and realizes he's been sleeping there. Brian dismisses him and says he's working on a new program and isn't ready to describe it yet, but says it's going to impress a lot of people.
At FBI Headquarters, Olivia talks with the doctor who confirms that Ella is okay. She's sure that the person responsible was watching her on the computer camera. Olivia figures that the killer was trying to send her a warning. Peter wonders why the killer is picking the particular targets.
In Evanston, IL, Miriam Rosenthal comes home and discovers her husband Mark dead at his computer, his brains liquefied.
Peter and Olivia are going to the laboratory and Olivia gets a report on the death. Peter spots an older woman standing outside the lab. He goes to talk to her while Olivia goes inside. The woman, Jessica Warren, wants to see Walter but Peter warns it's not the right time. He expresses his condolences for what happened to her daughter but Jessica insists she needs to see him. Peter refuses and goes inside.
Inside, Walter explains that the computer program amplifies the electrical patterns in the brain, and the hand is a hallucination brought on by the stimuli. Peter arrives and talks to Olivia, who knows Jessica is the mother of the woman who died in Walter's lab accident. Peter says Walter doesn't know and feels his father couldn't handle it. Olivia disagrees, thinking Peter is underestimating Walter. Peter storms out while Astrid comes in with a report on Mark Rosenthal. He married Miriam Dempsey a year ago, and Olivia connects her to Luke Dempsey. Olivia confirms that Miriam is Luke's mother and the victim is Luke's stepmother. She remembers that Luke mentioned his father and Greg's worked together.
In the lab, Peter is disconnecting the phone when Walter asks him if anything's wrong. Peter lies and Walter wanders off. Olivia comes in with the file on Brian Dempsey. He's a programmer who was fired by Greg's father six years ago.
They take Luke into custody but are unable to find Brian. He tells them to break Luke right away and Olivia warns he might shut down and call a lawyer. Olivia disagrees but Harris tells her to go after Luke. Olivia and Charlie confront Luke and show him photos of the victims, then demand to know where his father is. Luke asks for a lawyer and refuses to speak. Olivia decides to release Luke and follow him, ignoring Harris.
Once released, Luke immediately uses a FBI phone to call for a cab. Olivia listens in and gets the address. She and Peter follow the cab and en route Peter insists he knows more about Walter. Olivia still believes it'd be a good idea for Walter to get closure on the accident, but Peter insists it's none of her business.
They arrive at a warehouse and Olivia goes inside alone over Peter's objections. She refuses to call for help, concerned that Harris will use it as an excuse to make her look bad. At headquarters, Harris discovers that Olivia and Luke are gone and orders a GPS trace.
Olivia makes her way through the warehouse and overhears Luke confronting his father. Brian spots Olivia on the security monitors and tells his son to run. Luke leaves, while Olivia makes her way to Brian's workshop. The killer program starts running on the monitors and Brian gets the drop on Olivia, holding her at gunpoint. He tells her it's time to end things and points a second gun at his head. He looks at the monitors and starts to enter a trance. Fascinated, he insists on finally seeing his creation.
Outside, Peter hears approaching sirens and goes into the warehouse. Luke, armed with a pipe, confronts him but they hear a gunshot and run to the workshop. Olivia explains that Brian shot himself but Luke runs outside where Harris and his men capture him. As he and his father's corpse are taken away, Peter wonders why Luke protected his father. Olivia says that it was because Brian was his father.
Harris meets with Broyles and complains about how Olivia disobeyed him. Broyles defends Olivia's actions and tells Harris that he's pursuing a personal vendetta. He warns Harris off, but Harris notes that he has plenty of red tape.
Peter brings Janice to the laboratory and tells Walter he's there for him if he wants to end the conversation. Walter approaches Janice and admits he remembers her daughter Carla. She asks him if there was anything he could tell her about her daughter. Walter says she was a wonderful girl with a beautiful smile. As Janice cries, Walter embraces her and promises to tell her everything he can remember.
Rachel wonders what happened with Ella and Olivia assures her she wouldn't feel better for knowing. Ella comes in after brushing her teeth and gives Olivia a kiss. Rachel goes to tuck her in and Peter arrives at the door. He admits she was right about Walter and apologizes for snapping at her earlier. Rachel comes out and Peter says hi, and then leaves.