Sherri is out on the jogging path waiting for her fiancé Greg Winfield to come back from relieving himself. She hears him scream briefly and goes to investigate. Sherri finds him lying and steps in his bloody lungs, lying near his corpse.
Duke comes to see Audrey at her apartment with coffee but she wants to go to work. He points out that she might want to do something other than work since she knows she may disappear in 46 days. Once he finds his car keys, Duke suggests that she should take time off from the unusual and Audrey admits that the thought has crossed her mind. He finally hands over the car keys and realizes that she hasn't told Nathan about her fated disappearance. Audrey says that she's waiting for the right time and Duke admits that it'd be hard on him to live in Haven if she disappears and Nathan doesn't know why.
After getting the police call, Audrey meets Nathan at the jogging path and he offers her coffee. He brings her up to speed and they go over to talk to the coroner, Dr. Lucassi. Lucassi informs them that the lungs were neatly severed and removed from the body. However, there is no incision on the body and Lucassi suggests that he may have expelled his lungs through his mouth. As Nathan and Audrey leave to expand the parameter, a man takes photos of the crime scene, focussing on the lungs.
Back at the station, Nathan puts together a list of people looking for lung transplants. Audrey notices that Nathan has theater tickets on his desk and he explains that it's a murder mystery. He suggests that Audrey could go but she hesitates when she learned that it will be in a couple of months, and then says that she can't. When he wonders what's wrong, Audrey explains about the Hunter meteor storm and how Lucy and Sarah disappeared... and that she will be gone as well in 46 days. Before Nathan can pursue the matter, Lucassi comes in and tells them that the lungs they found by Greg's body lungs were necrotic and barely functional, meaning they couldn't have been his.
Nathan goes to talk to Sherri and she says that she talked to another guy about it, much to Nathan's surprise. He gives Audrey a description of the man, who called himself Tommy, and sends Glen the cop to get a detailed description and put out an APB. However, Glen tells him that they got an unusual disturbance call and they go to the house. The man from the station, Tommy Bowen, is there examining another body with a set of kidneys to the side. Audrey checks his ID and confirms he's with the Boston PD. He explains that he's there looking for the killer as well when he struck in Boston. As Nathan handcuffs him, they hear someone moving upstairs. Nathan fastens him to the railing and goes upstairs with Audrey. A woman is seated in the attic and she gives her name as Zoe Sellers and says that she called the police. They realize that she's in shock as she asks if her brother is okay.
At the station, Audrey questions Zoe and confirms that her brother saved him and the killer took his kidneys out through his mouth. Callahan arrives and suggests that Audrey talk to her about her relationship with Nathan but Audrey refuses, saying things have changed. When Audrey goes back to her office, she finds Duke waiting for her. He apologizes but she admits that he was right and she told Nathan what is going to happen. Duke tells her not to blindly accept her supposed destiny. Audrey points out that Lucy and Sarah didn't have a choice and Duke admits that he has no idea how to help her. He tells her to call if she needs anything and leaves.
Glen's nephew, Mark, comes in, and Callahan tells Glen to get a blanket for Zoe while she calls an ambulance. Once they go, Zoe suddenly jerks up, staring wildly around her.
Nathan calls Tommy's superiors and confirms that he's legit. He tells Audrey that they get rid of outside cops anyway that they can and they go to Tommy's cell. Tommy figures that they've cleared him of the crime and explains that his trainee, Paul, was the victim in Boston. The witnesses saw the killer wearing a Haven baseball jacket. Tommy came to town and monitored their dispatches until he heard the report on Zoe's brother. When Nathan refuses to cooperate, Tommy points out that as an inter-state crime he can call in the FBI. However, he says that he won't as long as they work with him.
Mark screams and the officers run to investigate. Zoe is attacking Mark and knocks Nathan and Audrey away, a fleshy tube extending from her mouth. Tommy arrives and knocks her out, figuring that she's on PCP. They figure that Zoe killed her brother, but Tommy points out that his partner's killer was a man so there must be at least two killers involved.
At the hospital, Callahan tells Audrey and Nathan that Zoe is in a coma and her organs are failing. Lucassi confirms that the diseased organs came from the same person and Audrey suggests that their Troubled person has diseased organs and needs to replace them. Since family members would have the closest organ match, the killer goes after a family member. If he fails to kill them, the victim's Trouble is triggered and they go through the same cycle. Mark is also undergoing massive organ failure, and Glen doesn't know of a family connection between him and Zoe. However, his sister used a sperm donor to become pregnant. Mark goes into collapse and Glen checks on him, while Tommy tells the officers that Paul didn't know his real father because his mother used a sperm donor.
The officers go to the Haven fertility clinic after Tommy confirms that Paul's mother went there as well. The administrator, Dr. Portenza, insists that none of the staff would have substituted their own sperm but Nathan insists that she turn over her staff and patient records and tells her he'll get a court order. Tommy goes with Portenza while Audrey and Nathan figure that the Troubled substituted his sperm so that he would have a ready supply of organs to harvest.
The killer, Harry Nix, goes to the high school and tracks down one of his "children," Miriam LaCroix.
Nathan and Audrey go back to the station and check the files, confirming that all of the victims are related. They figure that one of the janitorial staff substituted his sperm. The officers try to work out how the Troubled take the organs and figure that they extend a tube down their victims' throats, suck out the organs, and then spit out their own bad ones. Tommy comes in and overhears their conversation, but dismisses their theory as ridiculous. Duke arrives and tells Nathan that Audrey called him for help. Nathan wonders why and Audrey explains that they have twenty-nine children that they need to track down. When Nathan says that he'll handle it without Duke, Audrey takes the list and walks away. Duke goes with her and Tommy wants the truth from Nathan.
Miriam is walking home when Harry approaches her and asks to use her phone because his car has broken down. She refuses at first but finally gives in and gives him the phone.
Audrey and Duke check houses and end up at the LaCroix home. They spot Miriam down the road, getting her phone back from Harry. Duke spots the Haven baseball jacket and they realize that he's the killer. Harry shoves Miriam away and drives off in his car before they can stop him, but Miriam starts convulsing and they realize that her Trouble has activated.
Tommy doesn't believe in the Troubled but he figures that Nathan has persuaded himself that they're true. The detective doesn't care as long as it doesn't interfere with his investigation. Audrey calls in with the license plate and Nathan traces it to Harry's address. Tommy checks the records and confirms that Harry worked at the clinic until six years ago.
Duke and Audrey go to Harry's home and discover that he's already moved on. She finds photos of Harry with his family and they realize that he took his children with them because he needs parts.
Harry takes his wife Marjean and family to a friend but discovers that he's not home. He assures Marjean that everything will be fine and tells her that he loves her. Harry then suggests that his son Connor go the bathroom before they leave.
Nathan and Tommy meet Duke and Audrey at the Nix home. Nix's family disappeared the last time the Troubles were there and they figure Harry won't get far without getting more organs. When Tommy starts to call the Feds, Nathan stops him and says that they wouldn't know how to handle Harry. Tommy reluctantly agrees and they figure that Harry won't go after his children except as a last resort. They split up to check out Harry's two closest relatives.
Harry takes Connor into the woods behind his friend's house and explains that his father used to take him into the woods and tried to hurt him. He didn't let him do it but it changed him. Harry then apologizes to Connor for missing his last game and tries to control himself, saying that he'll be fine.
Audrey and Duke pull up to the house and find Marjean and her two daughters parked outside. She tells them that Harry took Connor into the woods as Nathan and Tommy arrive. They run into the woods and stop Harry from sucking Connor's organs out. Tommy stares in horror as Nathan knocks Harry away, while Duke confirms that Connor has gone into shock. Audrey tells Nathan to take Connor and Tommy away, saying that she only needs Duke, and Nathan realizes what she intends to have Duke do. He reluctantly agrees and takes Tommy and Connor away.
Once they leave, Audrey apologizes to Duke and he realizes that she wanted him with her so he could end the bloodline curse. Duke doesn't want the guilt on her but Audrey points out that Harry is dying and Duke can end the curse for good. She explains that she didn't want him there at first, but when she saw the baby photos at the clinic, she realized that Duke was the only one who could save hundreds. When Duke says that killing would make him a monster, Audrey tells him to walk away and she'll deal with it.
Later, Audrey meets the others at the morgue where they have brought all of the victims that Harry claimed. Tommy figures that he can't tell anyone what he saw because they'll think he's nut, but admits that Haven is a good little town. Nathan invites him back if he ever needs a change of scenery. Once he leaves, Nathan reveals that there is one additional victim. Her nose was surgically removed, her organs are intact, and she was killed with a bolt gun. The wound matches the one that in Roslyn's skull and Nathan tells Audrey that the man who abducted her is doing it. He promises that they'll find out who is doing it and why and Audrey walks away, shocked.
That night, Audrey returns to the station and Nathan catches up to her. He insists that they need to talk and admits that he doesn't understand why she's given up and now is asking Duke to kill people. Audrey points out that he didn't tell her about the tattoo he got and Nathan says that he got it to protect her. She says that she doesn't want his protection and Nathan walks away.
Later, Audrey meets with Callahan and tells her what happened. The psychiatrist says that Audrey pushed Nathan away on purpose and Audrey admits that she did to protect him .As they talk, Audrey gets a phone call and tells Callahan that she has to go.
Duke is drinking at the bar when Audrey comes in response to his call. She tells him that all of the children recovered and figures that Duke already knew it. Audrey asks him what happened.
As Duke walked back to the house, he saw Marjean embrace Connor and realized what was in store for the boy. As Audrey stepped away to call an ambulance, Duke went to Harry and smothered him to death.
Duke walks away from Audrey without saying a word.
Tommy is at his motel room when someone breaks in and tries to kill him. He shoots the man and then calls his boss and says that he's going to accept a job in Haven rather than come back to Boston and get killed. He then buries the killer's body in the woods.