Peter comes in to discover Walter giving LSD to a caterpillar. Astrid arrives and tells them that Olivia has gone missing.
Olivia wakes up strapped to a gurney being wheeled through underground tunnels. A man in an old man mask ignores her questions and takes out a syringe. He says "it" won't take long and after putting electrodes on her head, has his two assistant flip her over.
Broyles mobilizes the entire local FBI to find Olivia.
As Olivia's abductor inserts a needle into her spine, Olivia notices that he is wearing leather shoes with a white spot on one tip. He tells her not to move. Afterward, the abductor removes his mask: it's Mitchell Loeb. He goes back to the office. In the lab, Olivia asks the two assistants for water. When one of them gets it for her, she asks them to let her sit up so she can drink it. Once she's sitting up, she smashes the glass into one man's face, then grabs a scalpel and impales another man. She subdues the rest and runs out.
Broyles gets a call from Sanford Harris. Sanford tells him that they go back a long time and he's telling Broyles that Internal Affairs is sending him in to do a full review.
Olivia leaves the lab and subdues the man on watch. She takes a gun and then looks around. There are dozens of samples, including large slug-like creature. She takes several vials of a yellow powder and puts them in a thermos for safekeeping. She takes the unconscious man's phone and car keys and runs out, shooting one man in the process. She finds the SUV the keys go with and drives away, then calls Broyles and tells him to get men to the address of the building where she was held. She pulls over at an empty lot and buries the thermos in a pile of dirt, then drives down the street. The FBI agents arrive and agents get out of their cars, draw guns, and tell her to get on the ground. When she tries to run, they shoot her with a tranquilizer dart.
Olivia wakes up in a hospital room with a man sitting next to him: Sanford Harris. She's handcuffed to the bed and Sanford explains she's in Boston Hospital. He notes she probably didn't expect to see him and he wonders if she was satisfied with his conviction. He explains that his conviction on sexual assault charges was overturned and now he consults for Homeland Security. They've assigned him to review Fringe Division and question both her sanity and her loyalty. Sanford points out that John Scott was a traitor and she was associated with him. He then reviews the fact she recruited Peter Bishop, who has a criminal record, to get Walter Bishop out of the mental institution. She asks if she's under arrest and he gives her the handcuff key and tells her she won't be investigating her own abduction. He leaves her alone to free herself.
Back at her office, Charlie talks to an angry Olivia as she plans to go back to the address where she was held. Charlie tells her that the building was empty and the phone and car she took are clean. He tells her that there's a woman, Rachel, waiting outside for her, and Olivia explains Rachel is her sister. Olivia and Rachel hug and then Olivia greets her niece, Ella, who gives her a Magic 8-Ball. Olivia says she's working a case and will meet them later. In the elevator, she calls Peter to meet her outside and bring Walter with her.
At Harvard, Olivia explains what her abductors did to her and tells them she hid the samples. They go to get them and Walter notes that he can identify the substance.
Professor Stewart Kinberg is at Boston College giving an epidemiology lecture. He takes a drink of water but then starts to choke and falls over, convulsing. His teaching assistant Tara tries to help him and gives mouth-to-mouth, but he dies in a matter of seconds, his throat swelling. A slug like creature emerges from his throat and scurries across the auditorium.
Broyles calls Olivia, Walter, and Peter to Boston College and Walter determines that Kinberg suffocated. He has a theory as to what the creature is but says he'll tell them later. Peter is scanning the auditorium with an infrared sensor and picks up the creature's heat trace. As Walter talks about the Ebola virus slides that Kinberg was talking about, Peter and Olivia try to track down the creature. Walter finally captures it with a trashcan. At the lab, Walter determines the organism was developed from the same material as the samples Olivia stole.
At FBI headquarters, Broyles confronts Sanford and objects to his treatment of Olivia. Sanford warns that he isn't that impressed with Olivia and the Pentagon is concerned about how Broyles was abruptly put in charge. He insists it isn't a witch hunt but Broyles isn't convinced.
At Boston College, Olivia talks to Kinberg's assistant, Tara, who doesn't remember anything unusual. Olivia has been checking on Kinberg and he's been coming home after midnight the last couple of nights. Tara denies knowing anything and Olivia deduces that she and Kinberg were having an affair. Tara explains that she knew Kinberg was going to take a secret job with the Centers for Disease Control (CDC), but she wasn't supposed to tell anyone. He was being assigned to a task force to deal with nationwide epidemics.
Olivia takes the information to Broyles and reveals that Dr. Russell Simon of Cambridge was also hired. She thinks Simon is the next target and that the people involved are the same ones who abducted her. Broyles tells her that Sanford has put everything on hold but tells Olivia to do what she needs to do. Olivia calls Rachel and tells her she'll be late. Charlie comes over and she tells him he's coming with her. As they leave, Mitchell Loeb promises he'll be coordinating the investigation.
They bring Simon to FBI Headquarters and he tells them the CDC wasn't expecting him for three months. Nobody else knew he had taken the job. Sanford comes in and calls Olivia and Charlie outside. He's skeptical of devoting the expense to put Simon in protective custody, and Olivia says that Broyles didn't approve the expense. She warns that Simon will die if they don't protect him and he agrees to approve the protective custody. Peter calls Olivia and tells her they made a breakthrough: the yellow powder she stole consists of minute eggs, and they're activated by stomach acid.
Mitchell brings Simon a glass of water with yellow powder mixed in. Charlie comes in to see him but Simon starts to gag and then dies as the creature crawls out of his mouth. Charlie shoots it as Olivia arrives.
Walter is examining a full-grown slug and identifies it as a single-cell viral specimen based on the common cold. They figure that someone is showing off and Peter worries about Olivia. She says she doesn't care what happened to her and Peter says he cares about her being safe. As she leaves, Walter notes that she's beautiful but Peter doesn't know who he's talking about.
Olivia goes home and cooks supper for Rachel and Ella. She asks about Greg and Rachel admits she can't do it alone. Olivia tells her she needs to be strong for Ella and offers her house for them as long as they want. She wonders if there's something else Rachel isn't telling her, but Rachel says there's nothing else.
The next day at FBI Headquarters, Loeb promises Olivia they'll find whoever is responsible. He tosses her the Magic 8-Ball which she drops to the floor. As she kneels to pick it up, she sees the spot on his shoes: the same one her abductor wore. She tells Charlie her suspicions in private and needs his help because Sanford is watching her. Charles assures her he'll help.
Olivia goes to the Loebs' house. Meanwhile, Walter experiments with applying decongestants to the slug. Charlie arrives and explains to Peter that he needs someone who can break the law. Peter is glad to help and Charlie tells him they need a wiretap on Loeb.
Olivia starts to break into Loeb's house but Samantha Loeb arrives and Olivia quickly says she stopped by to see if she's okay after her husband's surgery. Samantha invites her inside for tea and Olivia says she's working on the case of a double-agent. The teapot whistles and Samantha goes to get it, while Olivia says she needs to use the bathroom.
At Harvard, Peter is making a call to set up the wiretap. Meanwhile, Samantha calls Mitchell, unaware that Olivia is going through their papers in the next room. Mitchell tells his wife to kill Olivia immediately and claim Olivia attacked her, as the agent is considered unstable. Olivia finds photos of the slugs in Mitchell's desk. Meanwhile, Peter completes the wiretap and hears Mitchell and Samantha discussing Olivia's murder and making it appear that Samantha shot Olivia in self-defense. He calls Olivia and warns her to get out of the house, while Samantha gets a gun and goes to the bathroom. Olivia isn't there, so she searches the house for her but Olivia Samantha gets the drop on her. Samantha drops the gun but breaks into tears and approaches Olivia. As soon as she gets close, she attacks Olivia, disarming her. The two struggle and both manage to grab their guns and fire. They fire simultaneously and Olivia kills Samantha, while Samantha misses.
At headquarters, they discover Mitchell has fled. Peter notes that Mitchell doesn't know about Samantha's death so they can send him a text message pretending to be his wife and using her cell phone. They send Mitchell a text message for him to go to a phone booth. As they wait, Walter tells Olivia that Peter was worried about her. Mitchell arrives and Olivia closes in on him while Broyles and Charlie close in. Olivia comes up behind him and shoots him in the arm. Olivia says he's under arrest but Mitchell just smiles, and she punches him.
Olivia and Charlie interrogate Mitchell, who refuses to tell them anything. He asks to see Samantha and Olivia refuses. Sanford and Broyles are watching and Sanford doesn't think Olivia will get a confession. Mitchell still refuses to talk and Olivia asks Charlie to leave them alone. Once he's gone, Olivia shows him a photo of his dead wife and tells him she pulled the trigger. Mitchell snaps and admitted he killed them, and asks if she knows what they're up against and what the rules are. Mitchell says they had a shot but she blew it, and he saved her. Mitchell tells her they were going to release her, but she doesn't have a clue what is going on.
Later, Olivia talks to Peter and Walter and wonders what Mitchell meant. Peter thinks Mitchell was disturbed but Olivia isn't so sure. She wonders why he didn't kill her but Peter says she shouldn't worry about it.
At home, Olivia dozes off with Ella lying next to her. Rachel comes in and kisses them both, and then turns off the lights.