In Hoboken, New Jersey, a man seems to be somehow manipulating a series of mishaps on the sidewalk. The commotion distracts a bus driver, who hits a blonde woman crossing the street. The man just walks away.
At Fringe headquarters, it's Olivia's first day back. Colonel Broyles tells Walternate that she seems like Olivia Dunham. Walternate confirms that, when tested, she responds like their Agent Dunham. Broyles still thinks that this is a huge risk. Walternate explains that Olivia can move between worlds without harm. The science division is working on some experiments, and they need her to believe that she's Bolivia so she'll go along.
Charlie briefs the Fringe team in the van. For two days in a row, a Liberty Metro bus has run a red light and killed someone. It's an interesting statistical anomaly. At the accident site, Agent Lee picks up a blue ballpoint pen near a mailbox. Charlie and Olivia are amazed - no one uses pens these days.
The mailbox is where a bike messenger swerved to avoid an old guy bending over, which led to the fatal distraction. Lee wonders if the pen started some kind of chain reaction.
Suddenly, Olivia sees Peter across the street! But then he isn't there. Later, at home, she tells Frank that she hallucinated the Secretary's son. He's worried, but Olivia insists she's fine.
Next day at HQ, Charlie says to Lee that, when Olivia was breaking down, she kept insisting that this wasn't her life. Charlie knows it sounds nuts, but what if that's true? Lee ponders, then decides that IS nuts. Charlie's not so sure.
Lee notices a pen, just like the one from the second accident, in a photo from the first accident. Farnsworth insists it's impossible to use a pen to set off a chain of events that leads to someone getting killed by a bus. Especially TWICE. But, wow, it's just happened again!
At the accident scene, Olivia sees another blue pen roll into view. The chain reaction isn't over! She spots a man, the one from Jersey, on the pedestrian bridge above. As an ambulance screams toward the scene, then a guy wearing headphones runs in front of it and gets hit. Olivia confronts the man on the bridge, but he escapes by leaping onto a passing delivery truck.
The man, Milo, goes home. His sister, Madeline, is worried about him. He mocks her concern and acts smug about how smart he is. Then she holds up a small plastic toy horse, a reminder of their past, and he gets rattled. She begs him to "follow the rules."
Olivia finds that both the second victim, Jillian Foster, and the first, Cole Arnett, were connected to brain research at Bryant Hospital. While investigating at Bryant, Olivia looks into a day room and sees . . . Walter! Then he's gone, but Charlie notices the patients are writing with blue ballpoint pens.
Bryant's chief medical officer, Dr. Levin, explains that many patients find pen and paper easier to use than digital interfaces. When he learns who the victims were - including the third, Jeffrey Mayer, who got hit by the ambulance - he tells Olivia and Charlie about a drug study aimed at increasing intelligence. Five months ago, Milo had an IQ of 56. Then he became a math genius - after one treatment. They gave him five, and each one exponentially raised his intelligence.
But the subjects get returned to their original mental states, and Milo didn't want to be regressed. So he killed Cole, his caseworker, and then Jillian, who planned to regress Milo herself. Mayer was a recovery specialist who brought back patients who went missing, but he hadn't yet been assigned to retrieve Milo.
Charlie and Olivia head out, as Milo watches. He is calculating their demise.
Madeline tells Olivia that she doesn't know where Milo is. They chat about siblings. When Olivia says her sister died, Madeline sympathizes, and Olivia seems momentarily confused. Madeline confesses that her brother is at the Patricia Hotel.
Charlie thinks it's a trap, and he's right. Outside the hotel, Olivia chases Milo, running past a flashing sign with the symbol of a hardhat-wearing worker breathing from an inhaler. Suddenly, a load of cement blocks falls toward her! But Olivia swerves, surprising Milo, who's using an inhaler. She grabs him, but she can't breathe.
Charlie charges up and shoots Milo in the leg, handing Olivia his own inhaler. Later, he asks why she broke protocol, ignoring the blinking auburn diamond that means compromised air quality. She doesn't know.
Olivia explains to Madeline that the effects of the drugs can't be reversed. Now the patterns that Milo sees are so complex, only a computer can understand him. Madeline tries to hold his hand and gives him the toy horse, but he just keeps muttering over his computer screen. Sad.
Frank, a virologist, is headed to north Texas to handle a smallpox outbreak. When Olivia is alone for a minute, Peter appears again. He tells her she didn't die today because Milo couldn't have known she didn't know the protocol. Olivia saw Walter, and thinks she's seeing Peter now, because she's not from this world. Olivia tries to shrug off the Peter hallucination, but he says she can't forget who she is. She can't forget THIS - and he kisses her.
Frank returns and asks Olivia what's wrong. She's just going to miss him. He says he'll be home soon, and leaves. Now Olivia really has something to think about.