An exotic dancer, Loraine Daisy, is in a bedroom with a man after sex. He goes into the bathroom and takes out a medical kit filled with surgical tools. He fills a syringe with an orange gel and takes out a refrigerated cylinder. However, Loraine stars screaming from the next room. He goes out and finds that her stomach is swelling and moving, getting larger with each second. He drives her to the nearest medical center, gets her out… and leaves her at the entrance. He drives away as she screams in pain. The doctors take her to the ER and ask her how many months pregnant. She informs them she isn't pregnant at all. She dies on the operating table and they perform a Caesarean to remove the baby… then stare at it in horror as the baby groans.
Broyles calls a meeting of a secret committee, including Nina Sharp, and informs them that they have a report of an anomaly. He briefs them on his new team, hoping they'll be more successful than the last one. Nina wonders if Walter's work lies at the root of the anomalies but Broyles notes Walter has been in an asylum for the last 17 years. He stands behind his decision to recruit Olivia, noting that she didn't hesitate to track down John.
Olivia is going over the files on John when Broyles calls and tells her to get the others and meet him at the medical center. She goes to the hotel and wakes up Peter, who finds Walter sleeping in the closet. He notes that a patient at the asylum used to sing Row Row Row Your Boat every night and he can't sleep without it.
They eventually get to the medical center and Broyles welcomes Peter and Walter, and then briefs them on the case. They haven't identified Loraine yet, and the baby was being transferred until the staff realized the newborn was… growing. Further, the baby was aging and within four hours it died of old age. Walter recognizes the symptoms and requests a lab, and Broyles reminds him he already has a lab. Broyles then briefs Peter and Olivia on the Pattern, a series of bizarre seemingly scientific anomalies. Astrid locates the hotel where Loraine stayed but Dr. Bishop refuses to go with Olivia.
Peter and Olivia go to the Loraine's hotel room and Peter finds some of the orange gel in the bathroom. Olivia realizes that only Loraine's belongings are there and has Peter open a cabin. The bed sheets are inside. She explains that she knows the killer from a case she and John worked on when she first joined the FBI. The killer went to the motel rooms in advance and replaced the sheets with leak-proof medical-grade linens. He picked up women, then gave them an orange-colored muscle paralyzer and then removed a piece of their brain through the roof of their mouth. She figures that the killer, the "Brain Surgeon," will strike again.
The killer, Christopher, goes to a bar and picks up a woman, Stacy.
Olivia goes to Charlie, who is preparing a memorial service for John. He wonders when Broyles will be done with her, and she asks if he knew about her and John. He admits he did and she's worried that she feels betrayed and can't trust her instincts. He agrees to provide her with the files on the Brain Surgeon.
Christopher takes Stacy to a warehouse and encourages her to look out the window at a bridge. When she does, he takes a hypodermic with the orange gel out. He start to kiss her, then injects her with the muscle paralyzer.
Peter returns to the lab where Walter is milking his cow. He's completed the tests on the elderly corpse and has confirmed that Loraine was impregnated by a man who is the result of experiments that Walter conducted 30 years ago. Walter has also remembered where he had parked his car. They go to a garage to collect it and Walter admits he has secret caches all over town. They get back to the lab where Olivia is going over the FBI files. They go through Walter's files on the pituitary gland, and Olivia reveals that the Brain Surgeon removed the pituitary gland of his victims. Walter reveals that advanced aging can be induced artificially by manipulating the pituitary gland. They find a related case file belonging to Dr. Penrose, a former research partner. They track him to Boston College where he teaches. As Olivia and Peter drive there, Olivia calls Charlie to have him run a check for any bodies with missing pituitary glands.
At the warehouse, Christopher prepares to remove Stacy's pituitary gland.
Olivia and Peter contact Dr. Penrose and show him a photo of the elderly corpse. He says that he didn't share his research with anyone, and found it so immoral that he resigned from his U.S. government research position. He's relieved that Walter was locked up, so that his research couldn't find its way into the government's hands.
Outside, Olivia and Peter are skeptical about Penrose's story and figure he's hiding something. Charlie calls them with word that Stacy's corpse has turned up, and he transfer it to the lab. They go there where Walter confirms he was involved in a plan to "grow" soldiers by artificially fertilizing women and then aging the baby to the proper age. However, they couldn't slow down or stop the aging process. Walter concludes that the killer is a "grown" human, and he needs the pituitary glands to treat himself and stay young. He lured Loraine to the hotel room and prepared to kill her, but they had sex first. The condom failed and the woman was impregnated and the fetus came to term in a manner of minutes. An angry Olivia realizes that now that the Brain Surgeon was scared off at the motel, he'll change his MO.
Christopher returns to the warehouse where he's greeted by… Penrose. Penrose calls him son and says they need only one more pituitary gland to save him.
Walter is working in the lab and suggests that try to find the last thing that Stacy saw before she died. Since she was given a muscle paralyzer, her nerve impulses were frozen at the moment of death. Walter suggests hooking up her optic nerves to a TV screen and seeing what she saw. Peter finds Olivia and informs her of what they have planned, but they need a piece of equipment that only one company owns the patent on: Massive Dynamic.
Broyles and Olivia go to the corporation and she asks him why he sent her on the case with John. In response he asks her a question: was she safe the last time she had sex with John. Suddenly Olivia screams in pain as her abdomen starts to swell…
… and she wakes up from her nightmare as Nina's assistant arrives. Nina offers Olivia her condolences on John's death and thanks her for not mentioning Massive Dynamic's name in connection with the investigation. She readily provides the pulse camera that they need for Walter's experiment. Olivia takes it to the lab where they hook Stacy's optic nerves up to the monitor through the camera, then start flashing through images.
Christopher goes to a bar and picks up a girl, Amy. He takes her to the warehouse and prepares to operate.
The team spot an image of a build and Astrid recognizes it. They run the image through the computer and identify the general location to the warehouse. They then go through satellite surveillance records and locate a gray sedan there at the time of both murders. Peter and Olivia go to the warehouse and find Penrose over the still-living Amy. Olivia hears Christopher makes a run for it and goes in pursuit. Peter tries to call for help but Penrose manages to increase the anesthesia feed. Amy goes into cardiac arrest and Penrose flees, while Peter tries to revive her without success. He calls Walter, who provides advice on how to improvise a defibrillator. Peter manage to revive her.
Christopher is fleeing through the warehouse district, aging with each step. Olivia finally catches up to him only to find him dying of old age. With his dying breath, Christopher explains he was an experiment and someone paid Penrose to create him, but Penrose grew to love Christopher like a son.
Later, Olivia returns the camera and Nina offers her a job at Massive Dynamic. She admits that her company has massive influence across the globe, in many cases superseding the government. Nina also hints that Olivia's acceptance would help her find out more about the Pattern.
Olivia meets with Broyles, who notes that Penrose was wounded in the escape but there's an APB out for him. He warns Olivia not to discuss the case with anyone, and then asks what Nina talked about. Olivia remains vague but mentions the job offer… and says she refused it and suggested Broyles would be paying her more.
Olivia tries to get Peter to sign government papers. Walter notes that he regrets the fact that Penrose represents the scientists who have tried to play God. He talks about Peter's medical files and the "truth" behind it, but Olivia doesn't know anything. Walter immediately passes it off as nothing, leaving Olivia puzzled.
That night at the hotel, Walter is counting numbers out loud and keeping Peter awake. Peter starts singing Row Row Row Your Boat to calm him down. Walter dozes off… and dreams of an unconscious Peter on a table in a laboratory with two other individuals in sealed tubes.