In Hoboken, New Jersey, on the other side, a man, Milo Stanfield, watches the street and counts out time on his fingers. He watches as a woman walks down the street, checking her watch, and gives money to a homeless man. She then stops at a flower shop to smell the flowers and goes inside to buy a bouquet. Milo then notices a bus approaching, a man drinking coffee, and a passing SUV splashing water near a mail box. Milo goes over and balances the pen on top of the mail box, then walks away as a bike messenger rides toward them. Milo follows the woman as she goes to the traffic light.
A taxi cab passes the mail box, splashing water and knocking the pen onto the sidewalk. The man drinking coffee goes to get it, and the bike messenger almost hits him. As people help him, the bus driver drives past. Distracted, he fails to see the woman cross with the light, and runs her down.
At Fringe Headquarters, Olivia arrives for work, believing that she's Bolivia, her counterpart. Charlie greets her and they joke back and forth and discuss her recent enforced treatment for psychosis. Meanwhile, Colonel Broyles and Secretary Bishop watch them from Broyles' office. Bishop insists that she is as real as the original, and has internalized all of her counterparts memories and responses. Broyles wonders if Bolivia has made contact, and Secretary Bishop assures him that she's focused on the task at hand. Colonel Broyles warns that putting an imposter on his team is too risky, but Secretary Bishop insists that Olivia needs to be immersed in her counterpart's life until she reaches a plateau and takes it on completely. When Broyles wonders what they have to gain, Secretary Bishop explains that Olivia can move safely between worlds. The science division needs her to submit willingly to some experiments, and once they learn what she knows, they can defend themselves. As Bishop goes, Broyles wonders what happens if Olivia's new identity doesn't hold. Secretary Bishop tells him that in that case, Olivia will no longer be necessary.
A Fringe team goes to investigate a second incident where a person was run over by a bus. As they arrive, they confirm that no oxygen is necessary. When Charlie and Olivia arrive, agent Lee is there and takes charge. His EMT warns that he has eight hours until he has to be back in the hyperbaric chamber in eight hours, or he'll relapse. Olivia talks with him, and she apologizes for pulling a gun on him. Lee assures her that they were good, and nothing could have happened.
The team examines the second victim, and Charlie confirms that she's Jillian Foster, who lives in Hoboken. Olivia talks to the bus driver, while Lee scans for environmental degradation. He notices the ballpoint pen and shows it to Olivia and Charlie. They haven't seen once since preschool, and it's clear that it's new. Lee gets an idea and suggests that pen set off a chain reaction. As they talk, Olivia notices Peter watching her from across the street. When she looks away for a second, Peter disappears. Her partners notice and Olivia assures them that she's fine. Lee insists that something weird happened, and Olivia agrees.
Olivia comes home to find her fiancé, Frank, making supper for her. She assures him that her first day back went fine, and notices that he's watching a broadcast on a smallpox outbreak in North Texas. Olivia tells him that she saw someone who looked like Peter Bishop, but dismisses it as a hallucination. Frank suggests that she shouldn't be on field duty, but she doesn't want to be removed from the field again. He volunteers to stay behind, but she insists that he go and reluctantly promises to tell Broyles if it happens again.
The next day at Fringe Headquarters, the team goes over the facts concerning the fact that each driver was distracted. There is no connection between the two victims, and Charlie dismisses it as coincidence. Lee notes that Olivia agrees with him, and Charlie says that he's not convinced that Olivia is entirely normal. In response, Charlie notes that Olivia kept insisting that she was somebody else, and suggests that Olivia is telling the truth. Lee dismisses his concerns, but Charlie warns that it's impossible to tell the two apart. Lee spots a ballpoint pen at the first crime scene and they realize the two deaths are no accidents.
The team takes the information to Agent Farnsworth, who insists that the odds that the two incidents are unrelated are 0.000. She notes that even she couldn't manipulate all of the variables at each incident, and then gets a report of a third accident. The team goes there and confirms that no one is dead. Charlie confirms that a dog distracted the driver and insists it was no coincidence. Olivia points out that no one has died. However, she sees a ballpoint pen roll out from under the bus and realizes that it's not over. She looks up at the bridge and sees Milo, studying the scene intently. An ambulance arrives and hits a jogger. As Olivia runs after him, Milo grabs a bike and throws it off the bridge and into the street. Olivia corners him but he casually jumps off the bridge and lands on a truck just as it swerves to avoid the bike. It drives off, taking him to safety.
At the Department of Defense hospital, Lee gets a two-minute warning to return to his hyperbaric pod. Olivia wonders how Milo managed to calculate all the odds, and Lee tells her to determine the connection.
Milo returns home and his sister, Madeline, says that they've been calling all day. She insists that she will call if he doesn't, but he calculates the odds and determines that she won't make a decision that would result in a negative income. He predicts what she's going to say, but then shows him a toy horse. Madeline notes that he's forgotten how to process emotions, and she made a mistake in signing him up. She tells him that he has to follow the rules and do what they say, and warns that he's overreaching. Madeline tries to get him to remember the toy horse, but he ignores it and goes to his room.
Charlie and Olivia call the witnesses, and she discovers that she needs a code that she doesn't remember from before her injury. Charlie brings up an incident on Coney Island when the rode a roller coaster, and corrects him when he test her. Olivia then notes that the second victim worked as a consultant at an electric company, and the first victim worked at a hospital. Both the hospital and the electric company are connected to the Ivon Medical Group.
Olivia and Charlie go to the hospital and talk to Dr. Levin. As they wait, Olivia sees Walter standing in a room, smiling at her. When Charlie comes over, he points out that all of the patients are using ballpoint pens. Dr. Levin arrives and ushers them to his office, and she asks him about the ballpoint pens. He explains that his patients have mental disorders, and find it easier to use paper and pen. Levin knows both victims, and explains that Ivon was conducting a medical trial at the hospital. They show him a photo of the third victim, Jeffrey Mayer, and he realizes that they're all tied together, and the person responsible is a patient.
Dr. Levin shows the agents footage of a study they conducted involving nootropics, smart drugs. They used the drugs to increase the intelligence of the test subjects. As they watch the video, Olivia spots Milo in the background. Levin admits that he's not surprised, and explains that after the first treatment, Milo was reciting pi to a thousand decimals. Milo received five treatments, and he was then released under a guardian. They then regress the subject to their original condition. The first victim, Cole Arness, was in charge of regressing Milo. When he was killed, Jillian offered to do it and was killed. They then hired Jeffrey Mayer to find the missing person, but he hadn't been assigned the task when he died. They confirm that Madeline was assigned as his guardian and head to her home. As they go, they're unaware that Milo is watching them, and calculating all of Olivia's future actions.
The agents go to Oyster Bay and talk to Madeline, who insists that Milo wouldn't kill innocent people. Charlie points out that Milo wouldn't consider his victims innocent. He goes upstairs to look at Milo's room, while Olivia notices some childhood photos. Madeline notes that she was close to her brother, despite their age difference, and Olivia talks about "her" dead sister. However, she seems uncertain that her sister is dead. Meanwhile, Madeline talks about how Milo never felt that he belonged, and that's why she agreed to the drug trial. Olivia warns her that Milo is dangerous, and asks her for any help she can provide. Madeline shows Olivia a goodbye note from Milo that says where she can reach him. Olivia thanks him and goes.
Outside, Charlie wonders if Milo planted the envelope, knowing that Madeline would give it to them and set a trap. They call Agent Farnsworth, who notes that there is no answer. Olivia decides to go to the hotel.
Milo is watching the hotel from across the street, and calculates Olivia arriving and being buried beneath concrete blocks. He then mentally rewinds the scene seeing the probabilities that lead her there and when they occur.
When the agents arrive, Milo shows himself and then runs down an alleyway at the precise time he foresaw. He "sees" himself luring her into a low-oxygen work zone, and being hit by the concrete blocks as she tries to use her rebreather. He leads her down a tunnel and into the low-oxygen zone. A forklift with concrete blocks approaches her... but she has no need for the rebreather. Olivia easily tackles the shocked Milo and then starts choking. Charlie arrives and shoots Milo in the leg when he tries to run, and then gives her a rebreather.
Later, Milo is taken away and Charlie asks why Olivia ignored the warning sign. He accuses her of being a daredevil and asks her not to do it again, and she agrees.
Olivia brings Madeline to see Milo, and explains that the drugs have been in his system too long. There's no way to regress him, and his thoughts can only be interpreted by a machine. Olivia admits that Milo no longer thinks in terms that they can comprehend, and Madeline goes into the room where he's kept. He ignores her even she takes his hand, and then goes back to his endless calculations. Madeline puts the toy horse down in front of Milo, but he doesn't notice it.
Secretary Bishop comes to see Brandon and notices that he has clothing from the other Peter. Brandon explains that he hopes to use it to help Olivia establish a link to the other side. Brandon notes that his test subjects have reacted poorly, and Secretary Bishop suggests that he immerse them in water. When Brandon asks if he misses being a scientist, Bishop insists that he is still a scientist... with a much larger laboratory.
Olivia watches as Frank packs. As he goes to check the phone, Peter appears and says that she didn't know the protocol. If she had stopped for oxygen, she would have died, and Milo couldn't factor that in. "Peter" tells her that she's not from this world. Olivia insists that he isn't real, but Peter tells her that he's there and he's a part of her she has to hold onto. He kisses her and then disappears. Frank comes in and wonders what's wrong, and she says that she's fine. Frank kisses her and promises that he'll be back as soon as he can. As he goes, Olivia looks nervous and scared.