In the Harvard lab, Walter doses caterpillars with LSD, while Peter comments on this sort of thing being the new normal. Astrid enters and asks if anyone has heard from Olivia... she's been missing since the night before.
A warehouse in an undisclosed location. Olivia is strapped to a gurney being wheeled down a warehouse corridor by two men. She demands to know who they are, but the men remain silent. A MASKED MAN, apparently the ringleader, ignores Olivia's protests and pulls a mechanical lever on the gurney that abruptly flips Olivia upside down --
The Boston FBI Office. Broyles briefs the agents on Olivia's abduction and announces that Agent Charlie Frances will be his second in command. This has now become a manhunt.
While Olivia hangs face down on the gurney, the restraining straps holding her in place, the masked man gives her a spinal tap injection and Olivia loses consciousness. Moments later, in another room, the man removes his mask: it is FBI agent MITCHEL LOEB ("In Which We Meet Mr. Jones," "The Equation," and "Safe").
Olivia is now right-side up and conscious again. She pleads for some water, but with the restraints on her head it is difficult for her to drink. Taking pity on her, the guard allows her to sit up -- and in a flash Olivia smashes the glass against the guard's head. She quickly releases the other strap, knocks out the other guard, and looks for an escape.
Back at the FBI, Broyles receives a phone call from an old friend, SANFORD HARRIS; a Marine officer Olivia helped to put away for sexual harassment ("Pilot"). Harris says that he will be performing a review of the Fringe Division. Meanwhile, Olivia makes her way through the warehouse and finds evidence of strange experiments. She grabs some samples from a laboratory and stuffs them in a stainless steel thermos. Once outside, Olivia uses the keyless remote she took from one of her guards to find a car and takes off.
On the road, Olivia calls Broyles to say she's escaped and tell him the location of the warehouse that needs to be raided. Before her rendezvous with the requested agents, she pulls over and buries the thermos in a vacant lot.
When the FBI agents arrive, Olivia is shocked when they pull weapons on her. One of the agents shoots her with a tranquilizer. When she comes to in a hospital room, she finds Sanford Harris sitting in the room. Worse, she is handcuffed to the bed. Harris explains that his conviction for sexual assault was overturned, and Homeland Security has assigned him to review Fringe Division. He also intends to investigate Olivia's history of questionable judgment, including her romantic involvement with John Scott and her recruitment of known criminal Peter Bishop and certified madman Walter Bishop. Harris forbids Olivia to investigate her own abduction.
At the Boston FBI office, Charlie tells Olivia that they raided the warehouse and found nothing. The car she stole is also clean, meaning they have no leads. As Charlie leaves, he also tells her that her sister RACHEL is downstairs waiting for her. It seems that her sister's visit has slipped her mind, and of course this is the worst possible day that she could be visiting. She greets her sister and niece, ELLA. Olivia has to rush off, but they plan to meet later at Olivia's apartment.
Olivia, Peter, and Walter go to the vacant lot where Olivia hid the thermos. Walter uses a portable microscope to examine the specimen inside, but before he can identify it...
Boston College. In a lecture hall; a biology professor gives a lecture about viruses, bacteria, protozoa, and fungi -- the four musketeers of the pathogenic world. In mid-sentence, he suddenly begins to choke and falls over. While his teaching assistant watches in horror, the professor's throat becomes enlarged, and what looks like a massive slug crawls out of his open mouth. As the slimy creature slithers across the floor, students flee the hall in mass panic.
Later, the lecture hall has been sealed off by the FBI as our team investigates the scene. The dead professor is identified as MICHAEL KINBERG, a renowned immunologist. As Peter calibrates a thermal imaging device to try and track the slug, Walter examines the dead professor. Peter locates the slug, which Walter ultimately traps under an empty trashcan.
Back in the lab, Walter takes a tissue sample from the slug and confirms that it is connected to the material that Olivia stole form the kidnappers' warehouse. Meanwhile, Broyles defends Olivia to Harris, but it is clear that Harris is now in charge and remains unconvinced that Olivia is the exemplary agent Broyles claims she is.
Olivia questions the professor's teaching assistant, TARA. Her guarded answers give Olivia a hunch, and she deduces that Tara was having an affair with Kinberg. Tara reveals that Kinberg was going to take a job at the Centers for Disease Control to coordinate national response to biological threats.
Olivia briefs Broyles on Kinberg's top-secret assignment. Another scientist, DR. RUSSELL SIMON of Cambridge, was slated to co-chair the committee with Kinberg. Olivia believes that Russell may also be a target and that the people who kidnapped her are behind the latest attack. Why kill an epidemiologist unless you want to start an epidemic?
On her way out of the office, Olivia talks to Mitchel Loeb, who says that he will be heading up the investigation into her abduction. Clearly, Olivia has no idea that Loeb is a double-agent. After Olivia and Charlie pick up Dr. Simon. In the middle of his questioning, Harris interrupts the interview. He is upset that he was not informed about Olivia's decision to place Simon in protective custody. Olivia appeals to Harris to set aside his feelings about her and do the right thing. Harris grudgingly assents.
Peter calls; Walter discovered how the slug-like creature works. The powder that Olivia stole from the warehouse is like eggs, which are activated by water and stomach acid. Meanwhile, Loeb pours yellow powder into a glass of water, and then delivers the water to Dr. Simon. Simon thanks him and takes a long drink. When Charlie returns to the room, he finds Simon beginning to convulse. Another slug emerges from his mouth, and Charlie pulls his gun and shoots it before it can escape. But Simon is already dead.
In the lab, Walter has made another breakthrough. The slug is in fact a gigantic single cell that has been infected and "supersized" by a cold virus. Someone is killing epidemiologists with the common cold!
At Olivia's apartment, Olivia and her sister catch up over a glass of wine. Rachel and her husband have recently separated. Olivia says she and Ella can stay as long as they want.
The next day in the FBI office, Loeb tries to cheer Olivia up by playing with the magic eight-ball that Ella gave her. But he accidently drops it, and as Olivia retrieves it she spots Loeb's black loafers -- and flashes back to when she was captive hanging upside down and saw the masked man's shoes. They are the same! Olivia realizes that Loeb was the kidnapper. She tells Charlie her suspicions. She needs Charlie to tap Loeb's phone because Harris is watching her every move.
Charlie goes to Peter and asks him for a favor that would be illegal for an FBI agent to do without a warrant: a wire tap on Mitchell Loeb. Meanwhile, Olivia stops by Loeb's house. But just as she is about to pick the front door's lock, Loeb's wife SAMANTHA arrives. Olivia pretends she was just checking in on Samantha to see how she is doing (after the events of "In Which We Meet Mr. Jones"). When Olivia excuses herself to use the bathroom, Samantha calls her husband. Loeb tells her that she needs to kill Olivia.
Olivia picks the lock of a desk in Loeb's study and finds evidence of the supersized cold bug. Just as Loeb tells Samantha where the gun is hidden, Peter's phone tap kicks in. He calls Olivia and tells her she's in danger.
Samantha and Olivia play a game of cat and mouse, until finally Olivia gets the drop on her. But Samantha knocks Olivia's gun away, leading to a brutal fight that leads to Olivia shooting Samantha in the head.
Broyles and the team try and figure out how to track down Loeb, who has disappeared. Peter realizes that Loeb doesn't know his wife is dead, so they use her cell to text Loeb a rendezvous location. Loeb arrives and Olivia arrests him. When Loeb gives her an evil smirk, Olivia hauls off and decks him -- a small bit of retribution for the kidnapping.
In interrogation, Olivia asks who Loeb is working for. Loeb is giving up nothing, just asking to see his wife. So Olivia pulls out the crime scene photos of Samantha dead. At last Loeb loses his cool, admitting to killing Kinberg. And then he starts raving about a plan that Olivia has ruined... that there is conflict with two sides in a war... that they were going to let Olivia go, that they were saving her... and that she has no idea what she is up against or what she has done.
After getting the confession, Olivia still tries to make sense of what Loeb was talking about. Peter surmises that Loeb was just playing head games, trying to confuse her. Olivia's not so sure. Back at home, Olivia falls asleep reading a book to Ella -- a picture of innocent and protector -- as Rachel turns out the light and tucks them in.