In Manhatan in the alternate Earth, architects Ted Pratchett and Pauline Hess are talking about the series of micro-tremors that have been shaking the building recently. Pauline leaves and another tremor strikes the building. The roof begins to cave in, the tremor stops, and the lights go out. When Ted looks around, he discovers that he is now partially merged with a support pillar… and another human body.
Olivia calls Peter and tells him that he and Walter are needed in Manhattan to investigate the earthquake. Broyles meets them and they go to the site where the paramedics are removing the nearby injured. There are no survivors. Both Olivia and Walter notice that the building appears to have been rearranged. They go inside and find workers merged with each other and parts of the building. Walter suggests there was some sub-atomic reaction that tore reality apart momentarily, and then reassembled. The paramedics find Ted, who asks them to call his wife. Broyles tries to calm him down and goes to call it in while Olivia asks Ted to describe what happened. Walter notices a painting on the wall and a brick wall beneath it. Meanwhile, Ted talks about the dogs howling and the micro-tremors. Neither Peter nor Olivia have heard of any micro-tremors. Walter discovers that the architects were working on a new annex to the Pentagon.
Broyles comes back and reports that Ted doesn't have a wife. Walter asks him to describe what buildings which buildings the terrorists attacked during 9/11, and Ted mentions the White House. Walter believes he knows what's going on. They notice a lump beneath Ted's short and open it to reveal… the head of another Ted. Both Teds die, and Walter explains that they are standing in two buildings: one is from the alternate universe.
The next day, Walter has the bodies sent back to the lab to find out what happened. Olivia realizes the collision resulted from Newton opening a doorway between the two universes, just as Bell warned her.
At the lab, Astrid finds Ted's body to disgusting to work on, despite everything she's seen with Walter. Walter has her go through the wreckage of the building and finds a Richard Nixon silver dollar and a model of a double-decker car. Walter pauses and then realizes what Newton did… and what's going to happen next.
Olivia and Broyles go over surveillance photos and discover that Newton and his people were on the site, disguised as construction workers. Walter goes and tells Peter and Olivia to come back to the lab immediately, but refuses to explain. When they arrive, Walter explains that twenty-five years ago, Harvard students somehow built a car around a statue. He admits that he and Bell did it, as part of an experiment to open a doorway. A car from another universe came through to balance the equation. Walter explains that since a building traveled from the alternate universe to their universe, a building from this universe will disappear, along with everyone inside it. Walter notes that he and Bell determined that objects passing from one universe to another have a distinct energy. The building on this side will take on a glimmer, but it's not visible to the human eye. However, Olivia saw the glimmer twenty-six years ago during the cortexiphan trials. She was the first child with the ability to see the glimmer and describe it as such. He explains that Olivia chose not to see the glimmer any more, but Walter can restore her ability. Olivia agrees and Walter needs to go to the day care center in Jacksonville where they conducted their experiment. If he needs to recreate the experiment, he can only do it there.
Olivia explains Walter's theory to Broyles, and that Bell bought the day care center and the military base it was sitting, and then closed it off. Broyles wonders if she plans to subject herself to Walter's experiments, and Olivia admits that she doesn't have a choice. She asks Broyles to track the incidents like Ted describes, and Broyles agrees to contact Nina Sharp and have her geologic department monitor for seismic activities.
Peter, Walter, and Olivia arrive in Jacksonville and go to the abandoned day care center. Inside, Walter asks her to pick out any of the sixteen objects that they brought over from the other side. She looks around but is unable to see the glimmer on any of them. As Walter prepares his experiment, Olivia sees her name written on the wall with the other children.
Walter and Peter enter a room filled with the chairs used to experiment on the children. As Walter goes through the boxes, he finds his old pair of glasses and admires his reflection. Peter goes outside to where Olivia is sitting on a swing. She admits that despite her excellent memory, she doesn't remember the day care center at all. Walter comes out and tells them that he's ready.
Walter wires Olivia into the equipment and explains that acute feelings can heighten the awareness and enhance perception. He treats her with cortexiphan and explains that the drugs will generate an obstacle unique to her. When Olivia faces the obstacle, it will elevate her perceptions to the proper level.
Olivia finds herself in a forest surrounded by tall trees. She senses someone else nearby and Walter and Peter watch as her life signs accelerate.
Olivia sees a figure moving through the trees as the sunlight disappears and the wind picks up. She goes into the woods and finds a small girl sitting against a tree. The girl says that she refuses to do what they want, and Olivia tells her that she doesn't have to do what she doesn't want to. The wind howls and the girl runs off. Olivia catches her and tells the girl that everything will be okay. The girl begs her to make them stop as something roars through the forest, and Olivia tells her that nothing can hurt her. She asks what the girl's name is, and the girl says "Olive." Olivia realizes that the young girl is herself.
The girl disappears and Olivia turns to find her standing behind her, her eyes glowing. Olivia wakes up and Walter says it worked. She wonders how he could have done that to children, but Walter insists they need to get to work. Olivia is still unable to pick out the items from the other universe, and is still angry at Walter for experimenting on children.
Nina goes to a building in New York City. As dogs howl in the background, she calls Broyles.
Broyles calls Olivia and tells her that it's starting. As Olivia walks down the hallway, she finds Walter watching old video footage of the experiments on Olive. He explains that the first time she saw to the other side, she set something on fire with her mind. Walter says that they were trying to help the children but Olivia says that she and the others were defenseless children. When he realizes what she's said, he explains that process didn't work because she's not a frightened child any more. They need a specific fear response, and the adult Olivia isn't capable of that. She's channeled her fear into anger, and to save the people in the building, she'll have to tap into that childhood fear again.
Olivia explores the day care center further and finds the room where Bell and Walter conducted their experiment. She crouches in the corner and Peter finds her there. Olivia admits that she's not frightened any more.
The team travels to New York and meets with Nina and Broyles. She warns that the tremors are increasing in frequency. Olivia admits that she can't sense anything, and Broyles explains that they're compiling satellite data to try to pinpoint the building that will disappear. Peter volunteers to help and he and Walter meet with Brandon. Walter warns that the events are random, but Peter suggests that mass is the key. The building that will disappear has to be exactly the same mass as the one that came over. Walter demands the necessary information to calculate the mass of every building in New York City.
Walter works out the calculations to pinpoint the target buildings. Walter's watch alarm beeps and he says that it's time, and it could happen at any time. Broyles admits that they still have 147 buildings that are possible targets, and several are hospital and clinics. There's no way they can safely evacuate everyone, and Broyles admits that they may have to let some people die in the disappearance rather than risk the lives of thousands more.
As Peter shuts down power to boost the computers, Olivia comes to see him. She admits that she's scared because she can't save the people under threat, and then realizes that's the key. She runs to the roof and looks out across the city, and spots a glowing building near the river.
Olivia drives toward the building and calls her information into Peter and the others at Massive Dynamic. She follows the glimmer and identifies the building as the Brayson Place Hotel. Broyles has the police and fire departments evacuate everyone from the building. She pulls up outside the hotel as people run outside in a panic. The tremors shake the area and she grabs the hotel manager and pulls him to safely. A vacuum springs up, pulling them back into the hotel. The manager grabs Olivia and Olivia grabs a lamppost. After a few seconds, the confluence dies down. They turn and look back, and find a huge crater where the hotel stood.
Later, Broyles watches a newscast about the incident, and how the government is claiming it was an unscheduled demolition. He wonders why her power finally activated, and she says that maybe it was just the right time.
Peter and Walter go home and Peter calls Astrid over to play Monopoly with Walter while he goes for a drink with Olivia. Walter is happy to hear that the two of them are getting together. Olivia arrives, having loosened her hair. Peter lets her in and she stares at him intently… and sees the glimmer. As Peter goes to get his coat, Walter realizes what she's seen and asks her not to tell Peter.