Roy McComb goes to St. Anne's Cathedral and goes into the confessional booth to meet with Father Kent. Roy asks Kent if God and the Devil can speak to people, and then says he sees things. In his mind Roy sees a man boarding a bus, carrying a case. He sits down next to a woman holding a blue back pack. When she sets the back pack down, the man notices and takes a gas mask and a metal cylinder out of the case. As the bus enters a tunnel, he puts on the mask and releases gas from the cylinder. The man takes the back pack and then walks off the bus.
Roy tells Kent that he wants it to stop and runs out. In the tunnel, the man meets with another one and they drive off. As Roy leaves, he drops a sketch of people on the bus, screaming in terror. In the tunnel, the policeman approaches the bus and looks inside: the inside of the bus has filled with a hard transparent substance, asphyxiating everyone inside.
Olivia and Charlie attend the funeral of John Scott and John's mother glares at Olivia as thunder rumbles in the distance. Afterward, Charlie assures Olivia she deserved to be there but she wonders, while at the same time is angry that John used her. Charlie tries to cheer her up as Broyles arrives to call them onto an assignment.
Walter and Peter are getting breakfast and Walter is medicating himself with homemade psychotics. Peter gets up to supposedly go to the bathroom but instead accosts a man who has been following him. The man says Peter was supposed to check in when he got home, but Peter takes the man's camera memory chip and warns that he'll come after the man first if anyone else finds out he's back. He gets back to the table where Walter finally tells him Olivia called. They rendezvous with Olivia and Broyles at the bus and Peter figures whoever it wanted to have some public impact.
The two men from the bus are in a church basement going through the woman's backpack but don't find what they're looking for. One of them makes a call and speaks in Latin, then leaves.
Roy is working in an escrow office and starts having visions again. He starts sketching the figure of a woman with bleeding hands.
While Olivia deals with the bodies, Walter and Peter take a sample of the resinous substance to the lab. Walter asks Peter to play a song but he refuses. Walter then asks about the man in the restaurant but Peter claims he doesn't know the man and it was a minor incident.
While going over the bodies, Olivia finds a video camera on one of the victims. Going over the recording, she spots the woman with the back pack, and determines it's not on her corpse. They identify the woman as Evelina Mendoza, an undercover agent for the DEA. She had a handler, Grant Davidson, and they bring him to FBI HQ for questioning. Three months ago Evelina was assigned to infiltrate a drug cartel and then called and requested removal. She claimed members of the Cartel were discussing The Pattern. She never met with Grant, who didn't know anything about what she was carrying. He asks to ID her body and takes its hand while Olivia waits outside.
Peter and Astrid have found a piano and Peter is playing when Olivia returns to the lab. They've identified the ingredients as being made from chemical compounds only available through Massive Dynamic. They're interrupted by a call from Charlie, who received a call from Father Kent. Olivia and Charlie go to Roy's apartment where they find sketches and models of dozens of attacks and other fringe incidents. All of the items are dated prior to the occurrences.
Charlie interrogates Roy at FBI HQ while Broyles confirms that only someone with foreknowledge of the events could have created the sketches and models. Meanwhile, Olivia meets with Nina, who notes they send the chemicals to dozens of labs and anyone could have stolen them. Nina offers her help and provides a list, and Olivia notes all the science and technology she's encountered have been controlled by Massive Dynamic. Nina parries by noting that her company is tied to most science and technology, but Olivia seems to be connected to the three most recent cases. Olivia mentions "attacks" and then notes that there was a similar incident in Prague, and Olivia would have known that if she had access to the case files.
Roy admits that he might be going crazy and draws or builds to get of the visions. He's been getting the vision for about nine months: the same time they became aware of The Pattern. Peter is convinced Roy is telling the truth and Walter suggests that Roy is psychic and in contact with the people responsible. Walter offers to prove it and while he prepares, Olivia confronts Broyles and insists she needs background on the cases she's investigating. Broyles notes that he won't be telling her everything for her own protection, and she'll be informed about what she needs to as it becomes necessary.
Walter, Peter, and Astrid take Roy to a hospital for a MRI scan to see if they can intercept the thoughts. However, when they switch on the machine, Roy's veins begin to swell. They switch off the machine and Walter realizes there's a magnetic compound in Roy's blood. The magnet in the MRI activated the compound.
Back at the lab, the team go through Walter's files and finds a notation on his work with William Bell, founder of Massive Dynamic. The two of them hypothethat there were waves of mental communication that they could tap into. The government wanted to use it as a "Ghost Network" to send clandestine messages invulnerable to intercept. Walter considered putting an iridium-based compound into a test subject's brain so they could tap into the network. Peter discovers that Roy was one of his father's experiments and is furious. Walter insists that the iridium he injected couldn't account for Roy's current condition, and someone else has perfected the Ghost Network. He figures someone only developed the network but didn't perfect the technique to grant others the ability to listen in. Walter believes they can redirect the transmissions to Roy's auditory cortex.
Walter needs a magnetic neurostimulator and Olivia and Peter go to his old house in Cambridge. Nobody's home and Peter breaks in to find the neurostimulator. They discuss their respective childhoods and find the device in a covered-over dumbwaiter.
As Walter administers the initial drug treatment, Roy wonders where he's seen him before. Olivia and Peter return with the device and Walter starts drilling so they can insert electrodes. Walter then starts redirecting Roy's sensory impulses but he loses feeling. Walter starts to lose his temper and then Roy starts speaking in Latin, relating the voices that he's hearing. Astrid translates it as an exchange occurring at a station in an hour. Someone on the Ghost Network says "it was on her the entire time." Olivia sees Roy's sketch of the woman with bleeding hands and goes to the morgue. She remembers Grant asking to see the body and discovers that Evelina's right hand has been cut open and something removed.
Olivia heads for the station and calls Broyles to send Charlie and a plainclothes team to meet her. Roy picks up Grant talking to his contacts and provides directions to Olivia via cell phone. Olivia tries to arrest Grant, but the other men shoot him and take the case. Olivia and Charles go after the man from the bus and corner him. He drops his gun and the case… then jumps in front of a speeding bus.
Broyles' team removes the item from the case: a small glass disk. They have no idea what it is and he says he's turning it over to the NSA for analysis. Olivia isn't pleased but Broyles reveals they've identified the killer and know how they communicate. He's happy with their success and turns over the files to her to read at her leisure.
Olivia returns to the lab and Ron says he's not receiving any more visions. They figure that the opposition shut down the Ghost Network after realizing it was compromised. Peter starts to play and Walter and Olivia both listen.
Broyles meets with Nina and turns over the glass disk. She mentions hiring Nina away and Broyles insists on protecting all of his agents. They both agree they want the best for Olivia, and he smiles and leaves. Nina takes the disc to an underground where a corpse is in a containment chamber and is hooked up to a computer. The technician takes the disc and notes it may be what they need to decrypt the information. Nina leaves as the technician studies the man in the chamber: John Scott.