In the prime universe, Walter is dismayed to learn that Peter is continuing to study the blueprints from the doomsday device. Meanwhile, fifteen people suffer retrograde amnesia after listening tonumber stations. The team discovers that there is a hidden signal buried in the radio transmission, leading them to a strange cube-like device which is assumed to be the cause; the device is revealed to be from the parallel universe, and the shapeshifter controlling them is using them to wipe the memories should the listeners solve the numbers in the station. Walter and Astrid solve the numbers; they are a series of coordinates throughout the world. When they arrive at a location in New Jersey, the team discover the coordinates lead to parts of the doomsday device. In the parallel universe, Olivia attempts to arrange another test, but a hallucination of Peter tells her she has to return home.
In the parallel universe, a twin frees his brother (guest stars Shawn and Aaron Ashmore) from amber. Walternate reveals that those who are trapped in amber aren't dead, but in suspended animationand those who are released will compromise its structural integrity. However, if someone was to reveal this, it could be damaging, so the Fringe Department is tasked to capture those responsible. Throughout the episode, it is revealed that one of the twins is a serial bank robber, and when the innocent brother was ambered, he posed as him. In the end, the bank robbing twin gets ambered. Meanwhile, Walternate experiments on Olivia by taking her to a sensory deprivation tank . Olivia succeeds in traversing universes temporarily. In the end, a hallucination of Peter convinces her who she really is.
In the prime universe, U.S. senator James Van Horn (Gerard Plunkett) is hospitalised following a car accident. After Newton arrives and shoots him in the face, Broyles discovers Van Horn was in fact a shapeshifter, who collected data on Fringe Division. Walter discovers that Van Horn is still alive at some degree and has another "brain" in his back. Before Walter can get to it, Newton activates asleeper agent, Ray Duffy (Marcus Giamatti) to extract it. When his mission is complete, Newton learns that Ray has grown attached to his family and kills him. Then, Fauxlivia and Peter capture Newton following a car chase. Knowing it may blow her cover, Fauxlivia visits him and gives him a suicide pill that causes him to bleed out mercury. In the end, Fauxlivia invites Peter to her home and sleeps with him in an attempt to draw his attention away from his growing suspicion that something is not right with her.