St. Anne's Cathedral, Boston. A man, ROY, sits in confession. He is deeply troubled and speaks in a trembling voice. Roytellsthe priest that the devil is speaking to him, sending him visions of horrible events, and his latest vision is about something terrible happening on a bus.
A Boston transit bus. A man in a business suit, ZIEGLER, gets on the bus and blends in with the other passengers. Moments later, he puts on a gasmask and releases a canister filled with smoke! While the otherriders panic, Ziegler calmly grabs a backpack belonging to one of the other passengers. The bus has come to a screeching halt as passengers choke on the white smoke filling the cabin. Ziegler steps off the bus and gets into a waiting car, as behind him everyone on the bus seems to freeze in place...
Roy, unable to finish his confession, runs out of the church, dropping a crumpled drawing of his last vision: a bus full of people, choking and dying as they try to escape.
Cemetery. A funeral is in progress for John Scott, Olivia's former partner and secret lover. The honor guard hands a folded American flag to John's mother, who stares directly at Olivia, almost as if she blames her for John's death. As the ceremony ends, Special Agent Broyles arrives and asks Olivia to come with him.
In a roadside dinner, Walter and Peter order breakfast. It seems like a normal moment between father and son until Walter begins to mix his own prescription drug cocktail - just a little something he whipped up in his lab to counteract the effects of the time spent in the asylum. Peter notices a guy at the counter who has been following him and goes over to confront him. The guy tells Peter he was supposed to check in when he got back in town. When Peter returns to the table, an unconcerned Walter announces that Olivia called about something happening on a bus. Also, he's decided he would like the pancakes.
Broyles leads the team to the bus, which sits in a blocked off tunnel. Our team sees the bus passengers suspended in the horrific death tableau, frozen within a misty translucent substance. Walter deduces that whatever suffocated them must have been released as a gas and then instantly solidified, encasing all of the passengers.
In what looks like a mysterious crypt, Ziegler and another associate dump out the contents of the backpack. They are searching for something, but they cannot find it. The associate takes out a strange satellite phone and speaks in Latin. Meanwhile, at his workplace, Roy has another vision. This time he draws a woman who appears to have stigmata - blood dripping from her hands.
In the lab, Walter ties to identify the substance from the bus, and Peter tries to help. To Peter's annoyance, the only thing Walter wants is for Peter to play the piano. Back at the crime scene, Olivia sifts through the personal belongings of the victims and realizes that a backpack is missing. The woman it was stolen from was an undercover DEA AGENT ANNA JIMENEZ.
Broyles and Olivia meet with DEA AGENT DAVIDSON, who says Agent Jimenez had stumbled on something involving "the Pattern," but what it was he doesn't know. Davidson then asks to identify the body. Olivia accompanies him to the morgue. Having just lost her own partner, she is sensitive to what Davidson is going through and gives him a moment alone with the body.
Back at the lab, Walter explains that the solid smoke was a silicon-based aerosol that solidifies into a solid when it comes in contact with the nitrogen in the atmosphere. Peter adds that Massive Dynamic manufactures the chemicals used in the solid smoke. But before Olivia can follow this lead, Charlie summons her to Roy's apartment; she's going to want to see what's there.
Roy's apartment. Charlie shows Olivia a room full of handmade models and drawings of pattern events, all of them gruesome and disturbing. All the drawings are dated before the incidents took place. It seems that Roy is seeing the future.
Roy sits in an interrogation room. Roy reluctantly explains that he gets visions in his head, and the only way to get them out is to draw or recreate them. This has been happening for nine months - about the same time that Broyles says the government became aware of the Pattern. Walter postulates that Roy might be receiving these thoughts from the people planning the attacks... he must be psychic! Moreover, Roy might not have any control over this ability, and the people sending the messages may not even know that Roy is receiving them. To prove his theory Walter asks to examine Roy.
Walter and Peter watch as Roy is placed in an MRI. As the machine whirs to life, Roy begins to scream in pain as ripples form across his skin and face. The high-powered magnets of the machine are pulling something out of Roy's skin!
Realizing that Roy must have metal in his blood, Walter returns to his old files and discovers that Roy is actually an old test subject. Walter was working on a military project to directly send messages into people's brain. To achieve this, Walter injected his subjects with an organo-iridium compound that would act as a receiver for messages sent over a secret radio frequency known as "the ghost network."
Walter hypothesizes that Roy is receiving transmissions sent by a group that has discovered and activated the ghost network. The messages are going intoRoy's sensory cortex, which explains why Roy is seeing and feeling the messages instead of hearing them. In order for Roy to "hear" the transmissions, Walter will need to shift the iridium compound to Roy's auditory cortex, a minor surgery. Minor brain surgery, Peter points out.
Peter and Olivia recover a neural stimulator that Walter had hidden years ago in the walls of their old house. Walter attaches the medieval-looking device to Roy's head. Then Peter shows Roy a series of images to determine where Roy is picking up the ghost signal. As Roy responds, Walter uses the neural-stimulator to shift the signal around Roy's brain. Roy first sees, then tastes, then smells the images until he begins to hear voices. But Roy doesn't understand; it sounds like gibberish. As Roy repeats the sounds he is hearing, Astrid realizes he is speaking Latin and translates for the group.
An exchange is being set up. The parties are going to meet at South Station bus terminal in an hour. The voice goes on to say that what they wanted "was on her the whole time."
Olivia looks at Roy's last drawing, the women with stigmata, and realizes that what the bad guys wanted was actually inside the undercover agent. At the morgue, Davidsondug something from the palm of Agent Jimenez's hand out. Davidson is a traitor! And now he is planning to hand over what he found to the people who attacked the bus.
Olivia, Charlie, and plainclothes FBI agents arrive at the bus station. As Astrid interprets what Roy is hearing, Peter relays it to Olivia in real time. Olivia spots Davidson carrying a metal brief case, but before she can reach him, another man, Ziegler, silently shoots Davidson and grabs the case. Charlie and Olivia give chase and corner Ziegler, but before they can cuff him, Ziegler steps in front of a bus and dies instantly.
Back at the Boston FBI offices, technicians remove a glass disk from the metal case that Ziegler stole. Broyles shows Olivia the glass disk. He doesn't know what is on it, but he knows that it is somehow linked to the Pattern.
Later. Broyles meets Nina Sharp of Massive Dynamic and hands over the glass disk, saying he'd rather not "go through channels." Then the two have a cryptic conversation about what is best for Olivia and her future.
Nina walks into a laboratory at Massive Dynamic and hands the disk to a scientist, saying that they have found another one. The scientist confirms that it is intact, and he should be able to break the encryption that is locking the data on the disk. The scientist then gestures to a computer monitor where streams of data are being downloaded. He has been able to stabilize the linkto another disk, and has been pulling data off it for the last 72 hours. The top of the data stream is labeled "John Scott," and Nina asks to be informed when the download is finished. Next to the monitor rests the body of John Scott, neural probes snaking back to the monitor.