At Stockton Harbor, Maine, lighthouse master Murray Hawkins guides a ship past and then tunes his radio to 6995 kHz on his short-wave radio as a music box tune starts to play. He sends a message on the computer. In Chinatown, New York, Shen Chan is working on a code when he gets the lighthouse master's signal. He tells his friend Dan Liang that he's close to cracking the code and logs on. Dan leaves in disgust.
In Merrimack County, New Hampshire, Becky Woomer tells her husband Laird that it's starting. He takes their baby with him and goes to make some tea, and Becky logs in with Shen, Murray, and 12 others. They go over the code numbering and Becky suddenly clutches at her head. Shen, Murray, and the others also begin to suffer head pains and convulsions, and then pass out. Murray wakes up when a boat calls in, but has no idea what's going on. Dan returns home and finds Shen staring at the code on the board. When Shen turns around, he looks at Dan, puzzled. Becky comes out to the kitchen and grabs a knife, and then demands that Laird tell her who she is.
Peter serves Bolivia breakfast in bed and kisses her. He tells her to check the entertainment section of the newspaper he's brought her, and she finds a pair of tickets to U2. She insists that she loves them and kisses him in thanks. Peter gets a call from Walter, who has discovered that he's running diagnostics on the destruction device from The Other Side. He warns Peter that it's too dangerous to experiment with, and hangs up. Peter explains what Walter said, and Bolivia gets a call from Broyles to check out the case.
The team meets and Broyles explains that fifteen people tuned to the same frequency all suffered retrograde amnesia at the same time, and the DOD believes it might be a terrorist attack. Peter and Bolivia talk to Laird, who explains that Becky was a moderator for a chat room group that listened to number stations. Meanwhile, Broyles and Walter examine Becky's radio equipment. Peter has Laird confirm that Becky recorded the broadcast, and that she was trying to crack some kind of code.
The team talks to Nina, who explains that number stations are mysterious broadcast points over 70 years old, which feature recorded voices reciting numbers. She plays one recording for them, and admits that no one has come up with a satisfactory theory to explain the broadcasts. Walter sarcastically suggests that Peter should play the recording of the broadcast that caused amnesia, and then says he'll talk to Becky when she's ready. He then tells the others that he can play back the tape without causing amnesia, and goes to get something from the child development center. Nina suggests that Peter watch Walter, and then asks Bolivia if everything is okay between the two of them. She tells Nina that Walter is blocking Peter's efforts to decipher the machine. When she suggests that Nina talk to Walter, Nina wonders why Bolivia doesn't do it, as she's usually more direct with him. Bolivia gives an excuse and Nina agrees to talk to Walter. She then gets a call from Broyles.
Homeland Security has traced the broadcast to a transmitter tower in Alford, Massachusetts. Someone broke in at the time of the transmission, killed the two staff members, and wired a metallic cube device into the station transmission equipment. Broyles and Bolivia lift a fingerprint from the device and take it to Harvard. Walter is using a child's Speak-n-Say to listen to the numbers broadcast using analog demodulation. He has located a hidden pulse wave that caused the amnesia, and attached it to the number broadcast. Peter figures someone used amnesia to stop the people who were close to cracking the code. Peter realizes that Walter used the soundboard that he was using to diagnose the Other Side's weapon, and Walter admits that he had more important things in mind then preserving his experiment.
Walter goes to his office and Peter follows him, and insists that they need to understand what it does. His father insists that he put a stop to it, and Peter explains that when he touched it on the Other Side, it responded to his touch. Before Walter can respond, Astrid tells them that they have a picture from the prints, and Bolivia has taken it to show Laird.
That night, a man approaches a transmission tower.
Bolivia shows Laird a photo of the man, who is known as Joseph Feller. He was last seen in Milwaukee in 1997. Laird has never seen him before. Peter and Bolivia get permission to look at Becky's computer and log books.
Walter talks to Becky and tests her responses and short-term memories. However, she admits that she doesn't recognize her baby or her husband. Walter assures her that the memories are still somewhere in her brain.
Peter goes over the list of people that Becky talked to, and finds the name of Ed Markham, bookstore owner. Bolivia doesn't recognize the name, and passes it off as a momentary lapse. Peter calls Markham while Walter comes in and talks to Bolivia. He admits that he knows what Becky is going through. Bolivia expresses her condolences, but Walter wants to focus on the case at hand.
Feller places a chip into a wireboard and then places it into a metal cube. He turns up the power and the box levitates into the air. Feller turns and leaves.
A plane flying overhead suffers sudden turbulence. The music box tone plays and a voice starts reciting numbers. The pilot clutches at his ears in agony.
The next day, Walter and Astrid learn of the crash, and confirm that the radio was tuned to the frequency of the second number broadcast. Walter is unable to get the recovered device to work, and Astrid tries to reassure him. Broyles calls to inform them that there's another cube at the break-in at the unmanned tower. Astrid suggests that Walter listen to some music to relax.
Bolivia and Peter visit Markham, who explains that he tried to decipher the code without success. He agrees to tell them what he knows in return for a promise of safety. Markham then explains that the number transmissions date back to the invention of the radio. He then gives them a book, The First People, with a writer's theory that there was another race on the planet long before humanity.
As Walter gets the second cube, Nina comes to visit and asks to talk to him privately. They go outside and share medicinal marijuana, and comment on how the college has changed. When Nina suggests that Peter continue working on the device, but Walter insists that it's too dangerous. She warns that Peter will continue to investigate whether Walter wants him to or not, but Walter warns that Walternate will assure that The Other Side's Earth will be the one to survive. He gave the blueprints to Peter to complete them. Nina insists that nothing is destined, and Peter needs Walter's guidance. She tells Walter not to become a fatalist now.
Peter and Bolivia drive back and Peter reads from the book. The author, Seamus Wiles, believed that a cataclysm wiped out the First People, who had discovered a vacuum, capable of vast destruction. Peter notices a number chart and Bolivia tries to remember the broadcast numbers. She finally recalls them with some effort, and Peter recites along with her. He explains that the number broadcasts match the ones in the calendar in the book, and somehow they are connected to the First People.
Back at the Harvard lab, Walter is intrigued by the First People theory, and the fact that they had created a vacuum mechanism. He believes that it all goes back to the Big Bang, and Peter suggests that someone translated the mechanism into a code, and someone wiped the minds of the people cracking the codes. Bolivia arrives with malassadas for Walter, and Peter finds a new transistor in the cube. It's a Polish military model, and only a few places store it. Bolivia tells Astrid to keep an eye on Walter and then drives away, claiming she's going to see Broyles.
Walter serves a sandwich and chips to Astrid, who is trying to decipher the code. He tells her that to break the code, she would have to think like the First People did. He mentions that they put nine days in a month. Astrid gets an idea and has Walter recite the days of the various months, and she believes that it's a cipher matrix.
Bolivia goes to an apartment building and meets with Feller. She tells him that they have a problem, and warns him that they found the new chip that he used. Bolivia says that they have their attention and there's no need to harm innocents. Broyles calls to tell Bolivia that they found Feller's address and on their way. Feller asks Bolivia for information on his next upload mission, and Bolivia says she has his next assignment.
Peter arrives with Broyles and a FBI team. They hear a gunshot and a second later Feller plummets out the window to his death, leaking silver blood. Peter goes to find Bolivia, and she claims that Feller came at her and she had no choice.
Astrid goes over the dates from the book's calendar and notices that the light from the window shines through the clear board she's using, and onto a world globe.
Peter runs to check on the shapeshifter and goes through his pockets. He finds a data storage unit but it's destroyed in the fall. Astrid calls them in and tells everyone that the numbers indicate latitude and longitude. The numbers indicates 22 specific locations on a globe, but there's nothing special at the indicated locations. Walter explains that they're looking something buried. The closest one is in Jersey City.
The FBI starts excavation on the site. Bolivia wonders if Walter is right about how the device could destroy one universe or the other. She asks what Peter would do if he had to choose, and only one Earth could survive. She insists that he'd do what he has to, to protect his world. Peter expresses concern for all of the innocent people on the other side, and insists that there's a way that doesn't involve destruction of either world. They're interrupted when the excavation team finds a rocky cylindrical object.
At the lab, Astrid continues her calculations and finds something startling. She calls Bolivia and tells her that the first piece is buried at Milton. She wonders if it's a part of the vacuum device, and Bolivia says that it is. Bolivia then tells them what Astrid has found out, and Walter says they have to find all of the pieces.
Later, Bolivia goes to the store and sends a message to her superiors, saying that the team has located the pieces. In response, she gets a message to initiate Phase Two.
On the Other Side, Brandon calls Olivia and tells her that Secretary Bishop has postponed the procedure, and it's on hold for the foreseeable future. Once she hangs up, Peter appears to her and warns her that she has to get out, because they have what they need. He tells her that she has to go home.