A woman, Sherri, is out jogging with her fiance Greg Winfield. When he goes out into the woods to relieve himself, she hears him scream and goes to investigate. Sheri finds him and is shocked to discover that someone has killed him... and removed his lungs from his body and left them lying nearby on the ground.
Duke visits Audrey at her apartment but she refuses to discuss what he told her about the Hunter meteor shower and wants to go to work. He suggests that she might want to worry about the fact that she's due to disappeared in 46 days when the meteor shower occurs, or at least take some time off. Audrey admits that the thought has crossed her mind and Duke realizes that she hasn't told Nathan what will happen. Audrey claims that she's waiting for the right time and is less than impressed when Duke jokingly claims that the only reason her disappearance would be a problem is that Nathan wouldn't let it rest once she disappears.
Audrey gets the call on the murder and meets Nathan at the jogging path. He brings her up to speed on the initial report and the coroner, Dr. Lucassi, tells them that the lungs were neatly removed from the body, but without an incision. Nathan suggests that they were pulled out through the mouth and that a Troubled may be involved. As Nathan and Audrey start searching the area, a man named Tommy Bowen is in the crowd and takes photos of the crime scene.
When they return to the station to check out leads, Audrey notices that Nathan has theater tickets on his desk. She points out that he's not a theater type but Nathan says that it's a murder mystery and invites her to come. When he says that it won't be for a couple of months, Audrey says that she can't. A clearly disappointed Nathan asks if something is wrong and Audrey finally tells him that she will disappear in 46 days, just like Lucy and Sarah did when she was them. Before Nathan can respond, Lucassi comes in and informs them that the lungs on the ground were necrotic and didn't belong to the dead man.
Nathan interviews Sherri but she tells him that she already talked to a police officer, Tommy Bowen. Nathan has no idea who he is and has Glen put an APB out on a man matching Sherri's description. Glen gives them a disturbance call and the officers head to the Sellers home. When they get there, they find Tommy examining a male body with a set of diseased kidneys to one side. They arrest him and confirm from his ID that he's with the Boston PD. Tommy tells them that he's there to find the killer the same as them, and they handcuff him to a post. Someone moves upstairs and Nathan and Audrey go upstairs to investigate. They find the dead man's sister, Zoe, in shock and she asks if her brother is okay.
When they take Zoe and Tommy to the station, Audrey confirms that Zoe's brother saved her by attacking the intruder. Haven's psychiatrist, Claire, comes in and asks if Audrey has talked to Nathan about their relationship. Audrey says that she hasn't, explaining that things have changed for her. She doesn't tell Claire why and goes back to his office, where Duke is waiting for her. He apologizes for his earlier comment but she tells him that she told Nathan just like Duke suggested. Duke tells her that she shouldn't just accept her fate, just like he isn't accepting his fate to become a killer, but admits that he doesn't know how to help her.
Glen's nephew Mark comes in for a visit. As his uncle shows him around, Claire runs out of the interrogation room and tells them that Zoe has gotten worse. The psychiatrist tells Glen to get Zoe a bandage while she calls an ambulance. In the interrogation room, Zoe suddenly snaps out of her shock and looks wildly around.
Nathan calls the Boston PD and confirms that Tommy is legit, and tells Audrey that they either recruit outside cops like herself or get rid of them. They talk to Tommy in his cell, and he explains that his trainee on the Boston PD, Paul, also died when his organs were extracted. A witness saw the killer wearing a Haven baseball jacket so Tommy came to Haven to investigate. Nathan refuses to cooperate with him and Tommy threatens to call in the FBI, pointing out that it's now an inter-state crime. However, he says that he won't as long they let him work with them.
As they let Tommy out, Mark screams from down the hallway and they go to investigate. They find Zoe attacking Mark, a fleshy tube extending from her mouth to Mark's. When Nathan and Audrey try to restrain her, she swats them away and Tommy knocks her over the head with his pistol. He didn't see the flesh tube and figures that she was high on PCP. The officers don't correct his misapprehension and figure that Zoe is the killer. However, Tommy points out that his witness identified the Boston killer as a man, meaning they have at least two killers responsible for the murders.
The EMTs take Zoe to the hospital and the officers meet with Claire. She tells them that Zoe has gone into a coma and her organs are shutting down. Lucassi has confirmed that the lungs and kidneys came from the same person and Audrey figures that their Troubled person is trying to replace their own dying organs. The killer seeks out victims that are likely to match his own DNA to avoid organ rejection, meaning that they are Troubled as well. If the attack doesn't kill them, the shock triggers their own Troubled curse, forcing them to seek out organs to replace their own.
Mark suffers the same organ failure as Zoe and they check with Glen, who doesn't know of a family connection between his nephew and Zoe. However, he tells Audrey and Nathan that his sister went to a fertility clinic and used donated sperm. Tommy confirms that Paul's mother also used a sperm donor to become pregnant.
Tommy confirms that Paul's mother went to the fertility clinic in Haven and he goes with Nathan and Audrey to talk to the administrator, Dr. Portenza. She insists that none of her staff would substitute their own sperm but Nathan tells her to turn over all staff and patient records, threatening a court order if she doesn't cooperate. While Tommy goes with Portenza to make sure she doesn't tamper with the files, Nathan and Audrey discuss the case privately and figure that the Troubled killer substituted his sperm years ago so that he would create a farmable bank of genetically-compatible "donors" that he could get organs from as necessary.
The killer, Harry Nix, goes to the local high school. He watches from his truck as a high school girl, Miriam LaCroix, leaves for the day.
Back at the station, Nathan and Audrey confirm that all of the victims had mothers who went to the fertility clinic. They figure that the killer worked as a janitor there years ago and sucks out his victims' organs by extruding a tube from his mouth down their throats, like the one that Zoe extruded. Tommy comes in and catches the tail end of their conversation and figures that their nuts. Duke comes in, much to Nathan's irritation, but the smuggler explains that Audrey called him in. However, Duke is disappointed to learn that Audrey wants his help in rounding up the twenty-nine remaining children from the fertility clinic that could be related to the killer. Nathan doesn't want Duke involved but Audrey ignores her partner's complains and goes with the smuggler while Tommy demands that Nathan tell him the truth.
Harry approaches Miriam on the street, claiming that his car has broken down and he lost his phone. He asks to use her phone and she proves reluctant at first but finally changes her mind.
Audrey and Duke go to the homes of the potential victims and are the LaCroix home when they see Miriam down the street. Duke realizes that Harry is wearing a Haven baseball jacket like the one that Tommy identified and they run down the street. Harry tries to suck the organs out of Miriam but has to drive away when Audrey and Duke come running. He escapes as Duke warns that Miriam is going into shock after the attack triggered her Troubled curse.
Once Nathan tells Tommy the truth, the Boston detective dismisses it as his imagination. However, he doesn't care as long as they go after the killer. Audrey calls in and gives them Harry's license plate, and Nathan runs it through the computer and comes up with Harry's name and address. Tommy checks the clinic records and confirms that Harry worked at the clinic until 2006.
Duke and Audrey go to the Nix home but discover that he has left with his wife and three children. They figure that Harry anticipated being discovered and was ready to move, and took his children with him because he needed compatible organs.
Harry drives his wife Marjean and their kids to the house of one of his "children," but no one is home. He tells Marjean that he loves her and then suggests that he take his son Connor into the woods to relieve himself before they leave.
Nathan and Tommy meet up with Duke and Audrey after confirming that the Nix family disappeared the last time the Troubles were in Haven. They figure that Harry will stop to get more organs and Tommy starts to call the FBI. However, Nathan tells him that the Feds wouldn't know what to do. Tommy, distrustful of the Federal authorities, agrees to hold off and they leave to check Harry's two closest donor-children.
As Harry takes Connor into the woods, he tells his son that his father used to do the same thing but tried to attack him. Harry admits that he stopped his father but something changed him in the process. He apologizes for missing Connor's last game and starts to shake as his organs shut down, and he tells Connor that he'll be fine.
Audrey and Duke arrive at the house and Marjean tells them that Harry took Connor into the woods. As Nathan and Tommy arrive, they run into the woods and stop Harry as he attacks Connor. Tommy sees the whole thing and realizes that Nathan was telling the truth, while Nathan knocks Harry away from his son. Duke confirms that Connor is going into shock as his Troubles manifest and Audrey tells Nathan to get Tommy and Connor back to the house. When she says that she only needs Duke, Nathan realizes what she has in mind and takes the others away.
Once the others leave, Duke realizes that she invited him along because she wanted him to use his own Troubled ability to end the curse. Duke doesn't want to become a monster but Audrey points out that they don't have a choice given that Harry is dying anyway and there's no other way to help the dozens of Troubled that Harry created to keep himself alive. Duke is the only one who can save all of Harry's donor-children by killing Harry and eradicating the curse from the bloodline. When Duke refuses, saying that murdering Harry would make him a monster, Audrey says that she'll find another way and tells him to leave.
Later, Audrey meets Nathan, Tommy, and Lucassi at the morgue, where all of Harry's victims have been brought in. Tommy admits that they were telling him the truth about the Troubled and figures that he can't tell anyone, but admits that their town has its charms. Nathan invites him back if he ever needs a job and Tommy leaves. Once the Boston detective is gone, Nathan shows Audrey one additional victim that they found. Her nose has been removed and she wasn't killed by Harry. Someone killed her with a bolt gun, the same weapon that was used to kill Roslyn. They go over Roslyn's x-rays to confirm the type of injury and Nathan warns Audrey that the mystery man who abducted her and Roslyn is the killer. Audrey wonders why her abductor would kill someone in such a manner and Nathan promises that they'll find out who is involved.
That night, Nathan approaches Audrey at the station and insists that they should talk. He wonders why she is giving up and asking Duke to kill Troubled. Audrey angrily notes that he didn't tell her about getting the tattoo. When Nathan explains that he did it to protect her, she tells him that she doesn't want his protection. Audrey then goes to see Claire and tells her what happened. Claire figures that Audrey pushed Nathan away on purpose and Audrey admits that she did it to protect her partner. The psychiatrist wants to pursue the matter further but Audrey gets a call and says that she has to go.
Duke is waiting for Audrey at his bar and invites her to have a drink. She tells him that all of the donor-children have recovered and asks Duke what happened. He explains that when he saw the shocked Conner after Harry's attack, he realized what he had to do... and went back and smothered Harry to death as he was dying from organ failure. Angry, he walks away from Audrey without saying a word.
Tommy is at his hotel room packing to leave when someone tries the door. Tommy draws his gun and prepares for his visitor. A short time later, he drives into the woods and then calls his someone and says that he's going to stay in Haven and take a job as a cop rather than come back to Boston and get killed. Once he's done with the call, Tommy starts burying his visitor's body.