Peter and Alt-livia's romantic breakfast is interrupted by a call from Walter, who is angry that Peter is still working on Walternate's machine. Broyles assembles the Fringe team to investigate the collective memory loss and they visit Becky's house. Her husband explains that she was listening to a "number station" and that the previous night's broadcast was recorded. The team visit Massive Dynamic to speak with Nina, who explains that number stations consist of artificially created voices inexplicably reading streams of random numbers. Walter wants to examine both Becky and her tape of the broadcast, and, as Peter escorts him out of the room, Nina notices the bad vibes between the father and son. Alt-livia explains the situation with the machine and suggests that Nina could convince Walter. Though Nina is surprised by Alt-livia's request, since the real Olivia is usually more direct with Walter, she agrees to speak to the scientist.
Broyles summons Olivia to Alford, Massachusetts, where homeland security has traced the broadcast to a radio tower. Inside, they discover a litter of corpses and a mysterious metal box, suspended in mid-air. Broyles determines that the box could be the source of the numbers broadcast and uncovers a fingerprint on the device. Back at his lab, Walter uses a Wah-wah pedal to separate Becky's recording into two waves - the first wave representing the numbers, the second the amnesia pulse. Peter suggests that the amnesiac trio had come to close to discovering the purpose of the number stations, so their memories were wiped.
Meanwhile, Feller breaks into another radio tower and constructs a second cube, which begins to emit a pulse. The pulse begins to affect the radio of an in-flight aeroplane, with the usual transmission being replaced by a stream of numbers. The plane's pilot holds his head and screams in agony. A television report in Walter's lab later reveals that Feller's second attack led to six deaths and twenty more cases of amnesia. As a frustrated Walter struggles to understand the cube, Broyles informs Astrid that the FBI have found the second cube that caused the plane crash. At his bookstore, Markham explains to Peter and Alt-livia that the number stations were an old hobby of his, presenting them with a book from 1897 that contains a theory as to where the transmission came from.
Nina arrives at Harvard to speak to Walter and the pair enter into conversation on a campus bench. She attempts to convince him that Peter is simply following his curiosity as they once did. When Walter protests that his son's experiments are dangerous, Nina reminds him of his own attempts to cross over into the other universe. However, Walter fears that Walternate could be using Peter to build the machine and so bring about the destruction of this universe. Nina encourages him to guide Peter and help in his mission.
In Olivia's car, Peter learns that the book tells of a great catastrophe that wiped out the first people, who lived prior to the dinosaurs. The first people were technologically advanced and had discovered "the vacuum" - the source of all creation and destruction. Reading on, Peter discovers a calendar and realises that the first string of broadcast numbers matches the numbers in the book. Arriving back at the lab, Peter shares his theory with Walter and Astrid, suggesting that if the first people created the vacuum, they could have translated the mechanism into a code. Examining one of the amnesia cubes, Peter discovers a transistor that is newer than the rest of the circuits. He claims that the transistor is military grade, meaning that sales would be regulated and whoever bought it would have provided a valid address.
Alt-livia leaves the lab, claiming that she is going to contact Broyles. However, she visits Feller and informs him that Peter is on his trail. She orders him to give up his mission, but Feller insists on continuing. As Broyles and the Fringe team arrive at Feller's apartment, they hear gunshots and the sound of smashed glass, as Feller plummets from his apartment window to the ground. His broken body bleeds silver, revealing that he was a shape-shifter. Peter realises that both Feller and his cubes came from the other side, and Broyles suggests that Walternate knows what the numbers mean and is trying to protect the code.
The excavation team discover something and pull it up out of the ground. At that moment, Astrid calls Alt-livia, explaining that the last set of co-ordinates leads to the house where the first part of Walternate's machine was buried. Astrid suggests that the locations could all hold parts of the machine and that the device is the "vacuum" created by the first people. As the excavated item is indeed revealed to be another part of the machine, Alt-livia replies, "Yes. I think they're one and the same." The Fringe team learn that there are 37 remaining locations, and Walter declares that they must assemble the pieces and find out how the vacuum works. He remarks, "Creation and destruction. I suppose we'll have to hope for the former."
Sometime later, Alt-livia enters the mysterious typewriter room, sending the message: "They've located the pieces of the device." The machine replies, "Well done. Initiate phase two." Meanwhile, in the alternate universe, the real Olivia is contacted by Walternate's assistant Brandon, who informs her that she does not need to submit to any more tests. Olivia has another vision of Peter, who warns her that Walternate now has what he wants from her. He insists that she is no longer safe and needs to find a way home.
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