A businessman, Bob Dunn, is preparing to cheat on his girlfriend Helen while she's out of town on a trip. As he prepares for the night, the new station runs a story on a local mutilation murder. His girlfriend calls and wonders why he didn't answer her call the previous night. As Bob goes to a bar, the Cavern, he tells her that he was busy and will see here when she gets in the next day, and he'll call later.
Entering the Cavern, Bob hits on one girl but fails, then picks up a brunette. He insists she's his kind of girl, and takes her back to his place. They start to kiss and then the woman grabs his neck and breaks it with one snap. Helen tries to call and gets no answer. The brunette checks herself in the mirror, noticing she has bright blue eyes. She shifts her jaw with a cracking noise. On the bed in the next room, Bob is dead, his spinal column ripped open.
The next day, Olivia chats with Neil and Helen, the parents of Graham, who is on a playdate with Ella. Rachel is there as well, and the couple talks about how they met through a matchmaking service that brings singles together, but not for marriage. As they talk about their relationship, Rachel gets served with papers informing her that her husband Greg is filing for divorce. Olivia is called away to Bob's apartment where Walter examines the corpse. Peter notices that Olivia is distracted but she refuses to open up, while Water concludes that a human being ripped open the spinal column using their teeth.
Olivia gives Broyles her report and tells him that Charlie is running a search for Bob's missing car. Before she leaves, Olivia asks Broyles for the number of his divorce lawyer. He gives it to her and wishes Rachel well.
Astrid and Walter go over the lab report on the two victims and determine that someone removed all of their spinal fluid. There are traces of syphilis bacteria on both victims, but Walter notes it's a variety that has been extinct for decades. Olivia contacts the CDC, and Agent Feiken comes to headquarters to inform her that the CDC shipped test samples of the bacteria to Lubov Pharmaceutical four weeks ago. When Olivia wonders why he came personally, Feiken explains that they've sent several other samples of contagious disease to Lubov. They also sent RD-390, a substance that can be used to make biochemical weapons... including the rapid-skin growth toxin the ZFT used.
Olivia takes a team to Lubov Pharmaceutical's address in the suburbs: a split-level home. Going inside, they find one man in a wheelchair: Dr. Nicholas Boone, busy saying open a dog's spine. They arrest him and ask about his connection to ZFT. Boone tells them that he knows who was dosed but won't share his information unless they help him recover his wife Valerie, who has been abducted by ZFT. He explains that the bioterrorist group is trying to blackmail him into helping them by using his wife as a hostage. Olivia confirms that Valerie went missing and wants to agree to Boone's terms. Boone provides an address and they confirm it's drawing heavily on the city's power supplies. Broyles gives the go ahead for an assault.
While Walter and Peter investigate Boone's lab, Olivia, Charlie, and their team head to the restaurant. En route Rachel calls Olivia to inform her that now her husband is filing for sole custody of Ella. Rachel insists that she'll take Ella and flee rather than let Greg have her daughter. Olivia tries to reassure her but has to break off when they arrive at the restaurant. Bursting inside, they arrest the staff and find a secret lab, but no signs of Valerie. Broyles informs Boone of what they've found, and the scientist insists on speaking to Olivia. Over the phone he directs her to the location of five vials of contagious samples, and he needs them to make an antidote. Boone then tells them the truth: the ZFT infected Valerie with the mutated syphilis and turner her loose, and she's the killer.
Peter finds a camcorder at Boone's lab with footage of the couple together. He notices something unusual.
Valerie picks up another man at the Cavern. They park and start to kiss, and he notices that she has a high body temperature. She apologizes, and then grows sharp teeth and rips his spinal column open. The next day, the police find the car. Broyles meets with Olivia and shows her the footage Peter found, and they realize what's wrong. They go to see Boone and note that three weeks ago, he had full use of his legs. Boone gives them the rest of the explanation: Valerie feeds on spinal fluid to survive, but the contagion generates high body temperatures that burned it out of her system so she needs to keep feeding. He tried to sustain her on his own spinal fluid as long as he could, until he ended up in the wheelchair. The ZFT have created the mutated syphilis virus as another demonstration of their abilities to other scientists, but could care less about the FBI. Now that Boone has the samples, he can try and make an antidote. However, he warns that the ZFT can duplicate his work and weaponize it.
Olivia agrees to let Boone work on the antidote and takes him to Walter's lab. Meanwhile, Charlie finds Bob's missing car. However, someone stripped it and took the GPS, which they could use to find out where Bob picked up Valerie. Peter offers to take Olivia to see his friend Mako, who runs a chop shop. They see him and Olivia manages to intimidate him into telling them where his people found Bob's car.
Walter and Boone work together using mutated penicillin to trump the mutated syphilis. As they work, the praise each other's intellect. Boone notes he knows who Walter is, but Walter observes Boone knows more about him than Walter himself does. Boone brings up the topic of the soul and wonders if he'll be judged one day for what he's done. Walter says that he often discussed the same thing with his former partner William Bell, but he figures there's still time for redemption no matter what one has done.
Olivia and Peter go to Weymouth where Mako's men found the car. They also find another corpse nearby. They take the body back to the lab where Walter and Boone are infecting a rat with the mutated syphilis and then testing the antidote. Astrid notices that all three bodies have a bar stamp from the Cavern. As they prepare to head out, the rat dies and Boone asks them to take Valerie alive so he can cure her.
Peter and Olivia go to the Cavern and scan the crowd using a thermal imager to spot Valerie's higher body temperature. At the lab, Boone realizes that to perfect the cure, he needs to bond it with spinal fluid, and his is the only compatible type thy can find on short notice. He insists that he's been measuring how much he has, and he has enough to make a donation. Astrid is skeptical but Walter agrees to take the necessary sample.
Peter and Olivia spot, and then lose Valerie. They finally pick her up again as she heads outside with a man. They call Charlie, who hits her with enough tranquilizer darts to keep her out for hours. Olivia calls the lab with the news, but Walter reports that Boone is having a stroke: he lied about how much spinal fluid he could spare, so that he could cure his wife despite the risk.
As Peter drives the SUV back to the lab, Olivia comments on how much Boone must love his wife. She wonders about Greg's treatment of her sister Rachel. Valerie suddenly wakes up, her system having burned out the drugs, and attacks Olivia. Peter manages to subdue her and they get to the lab. Walter administers the antidote and after a few minutes of excruciating pain, Valerie is cured. However, Boone has died.
Later, Walter gives Olivia a videotape that Boone made for her. On it, Boone explains that he was well aware he might die, but insisted on holding up his end of the bargain. He starts to give her the names of the people in the ZFT he knows.
Later, Olivia meets with Broyles at a bar, and tells him that among the names Boone provided was the man funding the ZFT: William Bell.
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