A VertusAir plane from Paris to New York is forced to circle due to the weather and a man is in his seat writing down notes on technology. His nose starts bleeding and the woman sitting next to him chats about how to stop a nose bleed. The man goes to the lavatory and takes a swab of his mouth and then tests it. Once he sees the results, he tells the stewardess that he doesn't have the time to explain. However, he needs her to collect as many tranquilizers as possible and everyone will die if they don't. While the woman calls the captain, the man tells him that he's going to lock himself in the lavatory. If they come back with the sedatives and he doesn't answer, they're to keep him locked in.
The man locks himself in the lavatory and starts screaming in agony. The air marshal comes over and orders the man to open the door. However, when he unlocks the door, the man is fine. At the airport, the man claims that he had a panic attack and apologizes for wasting their time. The TSA agents start going through his bags and the man starts convulsing as his nose bleeds again. They let him go to the bathroom and the agents find a pack of syringes and figures he's having a panic attack. In the bathroom, the man convulses as spines shoot out of his back. The marshals start calling the cops when the transformed passenger smashes through the door and attacks them.
Olivia is meeting with a Bureau psychiatrist, Dr. Anderson, and insists that she's comfortable forgetting the details of her life, and would rather focus on David Robert Jones. She complains that she's undergone dozens of tests and believes that she should be out looking for Jones. The psychiatrist wonders if Olivia has told her sister Rachel what she's going through and Olivia explains that Rachel moved back to Chicago with Ella to be closer to her ex.
Later, Broyles calls Olivia to his office and admits that the psychiatrists have no idea what to do with her. She insists that she can relearn what she has to and is fit for duty... until Broyles points out that Rachel is still married and has two children, including a younger brother. They've confirmed that 40% of her life isn't what she experienced, and says that she's not the agent they licensed.
Olivia returns home and Peter immediately realizes that it didn't go well. She explains that Broyles has suggests she take a leave of absence and Peter agrees, suggesting they go to Vermont. He gets a call from Lincoln saying they have a case, and he is reluctant to take it until Olivia tells him that it's okay.
Peter goes to the lab where Lincoln and Astrid are going over surveillance footage from the airport. Lincoln explains that Broyles has assigned him to take lead. When he mentions VertusAir, Peter recognizes the name from a case he worked in his timeline. Walter comes out with all of the birthday presents that he saved for his son over the years. Peter, touched, gives him a hug and thanks him. He then describes the case he dealt with, where Marshall Bowman was an undercover cop given a designer drug that rewrote his DNA and turned him into a giant porcupine and was killed when the plane crash. Astrid confirms that the passenger was Bowman but that the plane landed safely. They watch the footage of the creature killing the two air marshals.
At the airport, Walter examines the creature's corpse and is duly impressed. Meanwhile, Peter talks to Bowman's sister Melinda, who says that she last saw him a week ago. She wants to see her brother but he tells her that it's not a good idea. He then has her confirm that the pad he was writing on is in her brother's handwriting, and that it has something to do with not turning back once they get started. Melinda tells Peter that the last time she spoke to her brother, he seemed stressed.
Peter goes to the lab and tells the others that the sister is a dead end. Lincoln has confirmed that Bowman worked in the BPD crash unit and retired six years ago, and they figure he was working undercover just like the Bowman that Peter knew. Peter suggests they find Bowman's partner, who was infected and didn't know it, and he can't remember the name. However, he realizes that Olivia would and Lincoln says that Peter should give her a call.
Olivia confirms the partner's name was Daniel Hicks and gives them an address. As Peter and Lincoln drive to see him, Peter finally says that they should talk to Lincoln, and Lincoln says that it's Peter's Olivia. He explains how he had last his partner Robert, who had a deep loving relationship with his wife. Lincoln says that Olivia has the same relationship with Peter and says they should leave it at that. When they get to Hicks' house, they discover that Olivia is already there. Lincoln realizes that there's no point talking her out of it and knocks at the door, but they get no answer. He picks the lock and they go in, and discover that the house is in a shambles. Bags of medicine waste are all over the kitchen and the windows are blacked over. As they look around, they're unaware that something is watching them from the shadows. It finally attacks Lincoln, scratching him and slamming him into a wall, and then leaves as Olivia shoots it.
Back at the lab, Walter sutures Lincoln's injury while Peter examines the Bowman creature. He has no idea about the syringe contents that Bowman has, and points out that there are track marks on Bowman's arm. Olivia spots a tattoo and Peter has Walter take a look at it, while she apologizes to Lincoln. She figures that Lincoln would have called Broyles if Olivia hadn't been there, and that he did it to protect her. Lincoln assures her that it's all right. Astrid runs a name that Olivia gave her Conrad Etienne Moreau, and confirms that he's a scientist but died five years ago in a car crash. In the other timeline, Moreau was the one brokering the sale of the virus. Walter explain that the tattoo is a Sumerian cuneiform and Peter realizes that there's someone who can translate it, even though he won't remember them. Lincoln considers going with them but Walter says that he needs to finish suturing the wound.
Peter takes Olivia to Markham's Bookstore. Markham doesn't know them, and Peter and Olivia stage a conversation about the symbol. They pique Markham's curiosity and he offers to translate it. However, when he sees it, he asks if Olivia is one of "them."
At the lab, Walter tells Lincoln that he can't leave until he tries his peanut butter and bacon sandwiches... and because he may be infected by the creature from the house. Walter admits that he can't cure the intermediate stage and there's nothing he can do until the virus fully matures.
Markham finds a reference saying the symbol translates to "rebirth," and there have been rumors of a cult that is obsessed with the guided evolution of man. According to their web site, they want to mutate humanity by design and advance evolution.
Kate Hicks comes home, unaware that the Hicks creature is lurking in the shadows. She finally hears it moving and goes to it, recognizes it, and calmly examines its gunshot wounds after hugging it. Kate then gives it an injection and assures her husband how special they'll both be, like Adam and Eve.
When Peter and Olivia return to the lab, they go over the Sumerian prophecies. Walter hears them talking and says that it's perfect, and explains to Lincoln that he hadn't realized how much he longed for family. Meanwhile, Astrid finds a reference to mankind using guided mutation to achieve mastery over mankind, using advanced algorithms. One of the references is palindromic code, and Walter explains that he and Bell created a system of coding using palindromic codes. They go to see Nina, who says that she recognizes the number but explains that they haven't used the system since Bell died. She tells Olivia and Peter that they do a number of experiments using genetic hybridization. As she pulls the files, Nina points out that Olivia was pulled off of field duty, and admits that every version of her must be stubborn. She pulls up the file but discovers that the contents have been erased from the inside. The head of the project was David Robert Jones.
At the lab, Lincoln is eating the bacon off of Walter's sandwiches and admits that he doesn't like pork. Walter realizes that something is wrong and asks what else he hungers. He wants onion rings and cheesecake and Walter comes up with the solution. He has Lincoln call Peter and Olivia back, and tells them that the creature craves lipids: human fat. The medical waste bags contained fat removed via liposuction, and the creature eats it to fuel its transformation. Astrid starts making a list of plastic-surgery clinics that have had thefts of liposuction waste, while Peter wonders how the creature is getting around without being seen.
On the roof of her apartment, the Hicks creature picks up Kate, grows a pair of wings, and flies away.
Walter blends a cure for Lincoln to drink to cure the viral infection. He then tells Peter that the drugs are designed to manage the mutation schedule and keep it from running out of control. When Bowman couldn't get to his checked luggage, his transformation ran out of control. Walter has used Lincoln's blood to model the transformation sequence. Astrid and Olivia return and confirm that there was a robbery of removed fat at a surgi-center. Two of the guards were killed and the place has been under lockdown, so the Hicks creature will have to go somewhere else. The computer model shows the creature developing wings, and Peter figures that it will go after a surgi-center in a high-rise. There's only one, in Beacon Hill, and Lincoln says that he has to call Broyles. Peter is hesitant to do that, but Olivia has already called Broyles and told him they need backup, and he said he'd deal with her later.
Lincoln leads a team into the clinic and they don light-enhancement goggles to search the place.
At the lab, Walter waits nervously with Olivia and discusses the sleeping defense in chess. Olivia realizes that porcupines are nocturnal and has Astrid raise Lincoln and Peter on the radio. Peter finally answers and Olivia tells him to turn on the lights to blind the creature. As it attacks Lincoln, they turn on the lights and Lincoln shoots it. Kate attacks him and Peter shoots and wounds her, hitting her in the shoulder. She looks over at her dying husband and breaks into tears.
Later at the lab, Walter eagerly opens Peter's presents while Astrid cleans up the wrapping paper. Peter and Olivia arrive and inform them that Kate will recover, but she has no idea who created the serum because Bowman obtained it for them. They wonder what Jones was up to and where he's recruiting the people who want to transform. Walter suggests that Jones has a god complex and wants to take control of mankind's evolution.
Broyles comes in and talks to Olivia privately. She apologizes for disobeying orders and getting Lincoln injured, and promises that she'll listen to what he has to say. Broyles waits until she's done and then tells her that they've decided that if she's even 60% of the Olivia that they've known, they need her.
Melinda meets with her boyfriend, Marco, who is worried that something went wrong with Bowman's transformation. She assures him that they can be born anew, the two of them, as children of a new world. Together the two of them inject themselves with the virus.
On a tanker in the middle of the ocean, a man locks up two of the creatures along with dozens of other mutated human beings.