Three people listen to shortwave radios while signed in to the same chat room. Murray is a Maine lighthouse keeper; Shen is in New York City's Chinatown; and Becky is the chat room's moderator in New Hampshire. Each tunes into the frequency 6955 kHz. They hear a music-box-type melody, then numbers being recited. Shen has a whiteboard covered in rows of numbers. Becky switches on a reel-to-reel tape recorder. Suddenly, all three appear to be in pain. When it passes, they have amnesia.
The next morning, Peter brings Bolivia breakfast in bed - and tickets to U2. Walter phones, upset that Peter's still working on Walternate's infernal device. Then Broyles calls Bolivia about the amnesia cases.
At Becky's house, Broyles reports that 15 people using shortwave radios along the Eastern seaboard all got retrograde amnesia at around 10:45 last night. Walter finds Becky's reel-to-reel tape, and Peter explains that Becky's husband, Laird, said that she and her chat buddies listen to number stations. What?
At Massive Dynamic, Nina explains that nobody knows what number stations are or where they're from, but they've never caused amnesia before. Bolivia asks if Astrid can see the MD research. Sure, says Nina. She asks what's up with the Bishops, and Bolivia explains their friction over Walternate's machine.
Broyles tells Bolivia that a radio tower is broadcasting static on the same frequency as the amnesia wave. Plugged into the tower's machinery is a glowing, floating cube. It has magnetics inside and fingerprints on it. Broyles sends it to Walter.
At the Harvard lab, Walter shows Astrid and Peter how to hear Becky's recording without losing their memories. He splits the transmission with his Jimi Hendrix wah-wah pedal: The top wave has the numbers, and the bottom is some kind of pulse, which caused the amnesia. The cube is the source of the pulse. Whoever did this knew the victims were close to cracking the numbers' code and wanted it kept secret.
Peter and Walter argue about Walternate's device. Peter insists that they need to understand it. Astrid interrupts, saying that they found fingerprints from a suspect on the cube and are going to show his picture to Laird.
Laird doesn't know the suspect, Joseph Feller. He gives Peter and Bolivia a list of everyone Becky talked to about number stations - including Ed Markham, the oddball bookstore owner. Bolivia doesn't actually remember him, but she fakes it.
Near Baltimore, the pilot of a small plane accidentally tunes into another number station, then clutches his head. Later, in the lab, Walter frets that now there are six dead people, plus 20 new amnesiacs. Broyles phones Astrid; they've found another tower break-in and another cube. He's sending it over.
Markham tells Bolivia and Peter that these broadcasts supposedly existed even before radio was invented. Creepy. He gives them a book, "The First People," which will explain where the numbers came from.
Nina and Walter sit on a bench, smoking a joint and remembering their younger days of wild exploration. She asks why he's resisting Peter's own experiments, and Walter huffs that Walternate is using Peter to make sure his world survives. Nina says Peter needs his guidance.
The book explains that the technologically advanced first humans discovered the vacuum, the "source of all creation and destruction." Also, they had months with wildly different numbers of days. Peter asks Bolivia what were the numbers from the first broadcast? She struggles to remember (since she doesn't have perfect recall, like Olivia): 12, 34, 17, 9, 15 and 8, 42, 40. The same ones are in the book. Huh.
At Harvard, Peter digs into a cube. Astrid reads about the vacuum, and Walter muses on the universe, the endless cycle of creation and destruction. Peter thinks that the first people created a device and translated it into a code. Bolivia arrives with pastries, as Peter says a transistor was recently replaced in the cube. They can trace the buyer. Bolivia will go update Broyles.
But instead, Bolivia visits Feller, the suspect! She says replacing that transistor jeopardized the mission. He wants to continue it, but she doesn't want more innocent people getting hurt. Peter calls with Feller's address. They're on their way, with backup. The troops arrive and hear a gunshot. Feller crashes out a window, landing on the sidewalk and bleeding mercury. Shapeshifter! In the hallway, Peter hugs Bolivia, who acts panicked and says that she had no choice. He says the pulse technology is from the Other Side . . . so Walternate is the one protecting the code. Peter retrieves the shapeshifter's memory chip, but it's toast.
Later, Astrid - who's figured out the numbers - explains that the code is a coordinate system indicating locations around the globe. Walter thinks things are buried in those places.
MD digs at a location in Jersey City. Bolivia asks Peter if only one universe can survive, and you alone had to defend your side, you'd have no choice, right? Peter has to believe there's another way. A large cylinder is dug up, and the machinery inside reacts slightly to Peter's touch. Astrid calls: The last coordinates are in Milton, Massachusetts, where they found the first part of Walternate's device. She thinks Walternate's machine is the vacuum, and Bolivia agrees. Bolivia reports that there are 37 more locations. Walter says that they have to assemble the pieces and figure out how it works.
At the photo store, Bolivia types, "We've recovered it." Walternate responds, "Well done. You know what to do now."
On the Other Side, Brandon tells Olivia the Secretary is postponing today's procedure. They'll let her know when she's needed. Peter appears and says that whatever they needed from her, they have it. She's not safe here anymore. "You have to go home."