In Manhatan in the alternate reality, Ted Pratchett and Pauline Hess are working at an architectural form, discussing Ted's stash of real coffee smuggled in from Hawaii, and go over their plans for a Pentagon annex. A series of microtremors shake the building and they complain, but note that the news has said that they're harmless. Pauline leaves for the night, and another tremor shakes the building: a large one. The power goes out and Ted is thrown to the floor. When he recovers consciousness, he discovers that he has merged with a support beam... and someone else's body.
Olivia calls Peter and Walter and tells him that there's been a major Fringe event in Manhattan. When they arrive, Broyles explains what happened and that they haven't found any survivors. As they go inside, it's clear that the building has somehow merged with another building, and that the people inside underwent a similar transformation, merging with each other and parts of the building. Walter suggests that some kind of sub-atomic earthquake occurred, rescrambling the molecules of everyone and everything inside. As they talk, the paramedics find Ted, barely alive. Olivia tries to get answers from him and he describes the microtremors. No one is aware of any recent microtremors in the area. Ted asks them to contact his wife, but Broyles confirms that Ted Pratchett doesn't have a wife. Realizing what has happened, Walter talks to Ted and has him describe the events of 9/11. When Ted says that the White House was destroyed, they realize that he's from the parallel Earth. As Ted begins to gasp out his last breath, they notice a lump beneath his shirt. Opening it, they find... another Ted. Only the head, however. Both Teds die, and Walter admits that what they've seen is the aftermath of the same building merging with its other-dimensional counterpart.
Walter has the bodies shipped to the lab and Astrid is unable to bring herself to deal with them. He has her examine the material evidence and she discovers a Richard Nixon silver and a scale model of a double-decker car. Walter realizes what has happened, and what must inevitably happen next.
Olivia meets with Broyles and explains that Bell warned her about the fact that Newton would attempt to open a doorway between dimensions. They check the surveillance photos and confirm that Newton and his shapeshifter soldiers were at the site in the days prior to the event, disguised as construction workers. Walter summons Olivia back to the lab and explains that he and Bell conducted dimensional transposition experiments 25 years ago. The result was that they sent a car to the other dimension. Another one came back, partway embedded in a campus statue. Walter explains that there must always be a balance, and thus an equal exchange of mass. Since a building came to this Earth... another one will soon disappear. Transposed objects have an energy signature, a glimmer, and Walter and Bell were experimenting with children using cortexiphan to give them the ability to see the glimmer. Olivia was their first and most successful test subject, but she points out she doesn't see the glimmer any more. Walter concludes that she blocked out her ability, and they will need to restore it to pinpoint the building that will disappear. However, he insists that they need to go to the day care center in Jacksonville, FL, where he and Bell conducted their experiments.
Olivia checks and discovers that Bell bought the military base holding the day care center, and that the property now belongs to Massive Dynamic. She asks Broyles to start tracking seismic incidents, and he agrees to have Nina Sharp use Massive Dynamic resources to detect the tremors. He wonders if she is going to go through with the experiments again, and Olivia admits that she doesn't have a choice.
The team arrives at the day care center, which is long abandoned. They go to a classroom and Walter asks Olivia to pick out the transposed objects from the collection scattered throughout the room. She looks them over but is unable to see anything. Walter prepares to recreate the experiments and finds a room filled with the chairs where the children were held. While Walter finds his old pair of glasses and tries them on, Peter goes out to the playground and talks to Olivia. She says that she doesn't remember anything from this portion of her childhood despite her excellent memory. Walter comes out and tells them that he's ready. He wires Olivia up and explains that he and Bell believed that acute feelings could enhance the special perception. He injects her with cortexiphan and explains that she'll undergo a hallucination. In it, some form of unique obstacle will appear before her. Confronting it will raise Olivia's lifesigns and thus her special perception.
The drug takes effect and Olivia finds herself in a forest. The sunlight quickly disappears and the wind picks up, and she finds a ten-year-old girl sitting on the ground. The girl refuses to do what "they" want her to do. Olivia tries to reassure her but a shrieking noise emerges from the woods. The girl runs off and Olivia goes after her. When she catches the girl, she tells her that everything will be okay. It seems to help and the girl says that her name is Olive, and Olivia realizes that the girl is herself. The girl's eyes start glowing and Olivia snaps out of her hallucination. Walter insists that they've succeeded, but Olivia wonders how he could inflict the kind of terror that she saw in herself as a child. Walter insists that it was necessary and that they need to confirm if the experiment was a success. Olivia examines the classroom again but is unable to see the glimmer on the transposed equipment.
Nina's people sense seismic activity in Manhattan. She calls Broyles, who notifies Olivia. In Jacksonville, Olivia finds Walter watching footage of Olive during the experiments. He explains that when she saw the glimmer, it triggered a psychic episode that set the room on fire. He insists they were trying to help the children by giving them a special ability, but Olivia isn't impressed. Walter realizes that the re-creation has failed because Olivia is no longer a scared little girl, and that she channels her fear into anger. He warns her that to find the building and save whoever is inside, she'll need to find that fear again and use it. She looks around and finds the room she set on fire, decades earlier. When Peter tracks her down, she admits that she isn't frightened any more.
The trio returns to New York and go to Massive Dynamic. Nina warns them that the microtremors are increasing and they're running out of time. They're compiling satellite imagery to try and find the building, and Peter volunteers to help. He and his father meet with Nina's scientist, Brandon, who is trying to determine a pattern. Walter warns that there is no pattern and that the transposed objects switch at random. However, Peter believes that the items that disappear are equal in mass to the item that created the imbalance. Walter agrees and starts calculating the mass of the buildings in New York City to find those that match the first building. They narrow it down to 147 buildings, and Broyles warns Olivia that some of them are hospitals. The loss of life caused by an emergency evacuation could conceivably cause more deaths than those caused by the building disappearing, and he admits that if they don't pinpoint the building, they can't order a mass evacuation.
Peter is working with the computers to enhance their performance when Olivia comes in to see him. She's upset that her inability to draw upon her special perception is condemning people to death. Peter tries to reassure her and they start to kiss... and Olivia realizes that she's now scared because she's failing. She runs to the roof and looks across the New York skyline, and sees a building glowing near the river. She drives to the building and notifies Broyles and the others en route. They confirm that it's the Brayson Place Hotel and order an evacuation. Olivia arrives as the ground starts to shake. She helps the last man out, the hotel manager, but the building disappears and the vortex threatens to pull them in. Olivia grabs a lamppost and the manager grabs her, and she holds on long enough for the vortex to subside. They discover that a huge crater has replaced the hotel.
Later, Broyles and Olivia watch a newscast about the incident, which the government has successfully covered up by claiming it was a demolition effort. When he wonders why she finally regained her special vision, Olivia suggests that it was the right time.
Peter calls Olivia and arranges a dinner date, and then has Astrid come over to play Monopoly with Walter. Walter is happy to hear that they're dating, even though Peter insists it's just dinner. When Olivia arrives, she looks at Peter... and her special sense lets her see that he's from the other Earth. Realizing what she's seen, Walter talks to her privately and asks her not to tell Peter what she knows.
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