On an airline flight, a man's nose starts bleeding. He tests himself in the bathroom, then urgently warns two flight attendants that everyone's in danger. He locks himself in a bathroom, bleeding and convulsing. Finally, an air marshal orders him to come out. He does, and seems fine.
He tells TSA investigators that he hates flying and freaked out because the landing was delayed. Flinching, he heads to the bathroom. In his luggage, the agents find a case containing syringes and drug vials. The man transforms into a spiny creature and bursts violently into the room.
Olivia would rather chase David Robert Jones than talk to an FBI shrink, but she has to prove she's fit for duty. Asked about her sister, she says Rachel moved to Chicago with her niece, Ella, so Ella could be closer to Rachel's ex. Later, Broyles informs Olivia that her sister's still married - and Ella has a little brother, Eddie. Forty percent of what she said about her life is incorrect, which to the 10th floor means she's not the agent they licensed.
At home, Olivia complains that she can't even consult on cases. Peter suggests a vacation, but then Lincoln calls.
At Harvard, Lincoln tells Peter about the incident on Vertus Air. Peter asks was it flight 718? Yeah. He recalls a case from his timeline (Season 1's "The Transformation").
Suddenly, Walter shouts, "Happy birthday!" He has wrapped gifts, one bought every year to help him deal with losing Peter. He knows that it's not Peter's birthday, and that Peter's not HIS Peter, but this is close enough. Touched, Peter hugs Walter.
Peter's case involved Marshall Bowman, an undercover cop dosed with a designer virus that transformed him into a giant porcupine. The plane crashed, and he burned. Astrid confirms it's Bowman, but this plane didn't crash.
However, Bowman died after busting out of the bathroom. At the scene, Peter questions Bowman's sister, who insists that she knows nothing. Peter says Bowman's partner was also infected. Olivia would know the guy's name. Lincoln reluctantly says call her.
As they drive to the partner's home, Peter invites Lincoln to talk about Olivia. Lincoln knows she's Peter's Olivia, though he doesn't really understand it. He bows out graciously, despite his obvious disappointment.
Against Broyles' orders, Olivia's at the partner's house. Inside, they find bags marked "Medical Waste." Then a creature attacks! It escapes - and Lincoln gets scratched.
At Harvard, Walter tends to Lincoln as Olivia tells Peter no one saw the thing flee. This case isn't exactly like they remember: Conrad Etienne Moreau, the scientist involved before, died five years ago. Walter says a tattoo on Bowman's arm is cuneiform, probably Sumerian, but he's not sure what it means.
Peter tells Olivia that an old friend could help, although he doesn't know them anymore. Walter makes Lincoln stay to get stitched up as the couple visit Markham's Used Books and gently con Ed into deciphering the symbol. It means renewal or rebirth - and it's the mark of a cult obsessed with the guided evolution of man, or mutation by design.
Now Walter won't let Lincoln leave. He just made peanut butter and bacon sandwiches! Also, Lincoln may be infected. Don't worry, Walter has an 80 percent chance of curing him. Lincoln is not reassured.
A woman encounters a porcupine-creature in her apartment - but she knows him. She tenderly gives him an injection.
Astrid finds a paper about encoding foreign genomes with retroviral DNA. Walter notices the file number's a palindrome (it reads the same forward or backward), and remembers he and William Bell once created a palindrome-based filing system. They visit Nina at Massive Dynamic. She says the number corresponds to an old project, but the contents have been erased. The project manager was David Robert Jones.
Lincoln devours the bacon from Walter's sandwiches, then wants more. Walter, inspired, calls everyone back. Agent Lee is infected, but now he understands that the creature craved lipids to fuel his metamorphosis. The medical-waste bags contained human fat, probably from liposuction at a plastic surgery clinic. Peter wonders how these creatures get around without being seen.
It's because they have wings. Carrying his woman friend, the creature from the apartment flies over the rooftops.
Walter cures Lincoln. He says that the drugs the TSA found help manage the transformation. Bowman died because he couldn't get to them. Walter's creating a computer model of the process; Peter sees wings sprouting on it and asks how many clinics are in high rises? Just one. Olivia says Broyles is sending backup to the clinic - and he'll deal with her later.
As FBI troops invade the darkened clinic, Olivia remembers porcupines are nocturnal. She phones Peter and says light will flush out the creature. The lights blaze on as it dives at Lincoln. He shoots it dead - and its companion attacks him! Peter shoots her. She lives, but she doesn't know who created the serum, which Bowman provided.
So ... what's Jones up to? How's he recruiting people? And who would sign up? Walter says human evolution, depending on who you talk to, is either a miracle or an accident. Maybe Jones wants to take control of the situation.
Broyles reinstates Olivia, noting that a Fringe Division with an Olivia Dunham is better than one without her.
Elsewhere, Bowman's sister and her boyfriend start the injections.
Aboard a freighter somewhere at sea, two porcupine-creatures growl in a cage. A man locks them in, then passes cages containing a giant tarantula, rattlesnake, and other beasts. Outside, he locks a heavy door. It's marked with that same Sumerian symbol.