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When a jogger finds her fiancé dead in the woods with his lungs lying next to him, she's horrified and calls the police. Audrey throws herself into the case, partially to avoid telling Nathan about The Hunter and her possible disappearance.
Naturally, Nathan and Audrey suspect a Trouble is responsible, especially when they realize that there are no incisions in the dead body and that the lungs at the scene do not even belong to the deceased. Things get even odder when Nathan attempts to interview the dead man's wife and finds out that someone named Tommy has already interviewed her.
That particular mystery is short-lived. Nathan and Audrey find "Tommy," a.k.a. Detective Thomas Bowen of the Boston Police Department, at the scene of another organ theft. He's chasing the same killer. They also find Zoe, a young girl who appears to be in shock over her brother's murder. After being interviewed, however, Zoe moves from distraught to violent.
Once Audrey and Nathan are able to confirm that Detective Bowen is who he says he is, they decide to partner up and, after a bit of deductive reasoning, they discover that all of the victims are related. Audrey comes up with a theory: Maybe the killer's "trouble" is that his organs fail and he needs the organs of a compatible family member to replace them.
Eventually, they trace all the family members to a single sperm donor at Haven's Hope Fertility Clinic. It turns out that the killer, Harry Nix, replaced the sperm of legitimate donors with his own sperm in order to keep his supply of children or new organ donors, plentiful.
Much to Nathan's chagrin, Audrey calls in Duke to help with the search for the killer's twenty-nine kids. With Duke's help, Audrey finds one of Nix's kids just as Nix is about to attack her.
Feeling the noose tightening around his neck, Nix packs up his family and makes a run for it but doesn't get far before he needs to acquire more organs and decides to use his son as a donor. Audrey, Nathan, Duke and Tommy all converge on Nix, and stop him, but they are too late to stop the "trouble" from affecting Nix's offspring.
What Audrey wants is for Duke to kill Nix and therefore end the "trouble" for good. Duke refuses at first, but ultimately feels guilty about what might happen if Nix's children start their own killing spree. He kills Nix, but he holds Audrey responsible.
Meanwhile, Dr. Callahan urges Audrey to talk to Nathan, Duke challenges Audrey not to simply give in to her destiny, Nathan is confused by Audrey's reluctance to tell him about her upcoming disappearance and, even after learning about the "troubles," Tommy decides to stick around in Haven after someone from his past tries to kill him.