Forest Lambert is closing up his store when someone starts yanking at the door. Forest tells him to push and the man barges in and runs to the freezer. Forest is shocked to find that the man is naked and savagely tearing at the raw meat. The man roars at him and he runs away in terror.
Duke stops by Audrey's apartment to help her install new locks just in case her abductor stops by again. She fills him in on what they found in the Colorado Kid's grave. She wonders about if he is really still alive and if he and Lucy Ripley were in love. Nathan arrives and objects to Duke's presence. He accuses Duke of being the Hunter, but Duke insists that he would never hurt Audrey. Nathan tells Audrey about the situation in the store and they head for Nathan's truck. Nathan orders Duke to stay away from her, but he refuses and vows to find out what the Hunter is.
They arrive at the store and Forest says the naked man was raiding the freezer all night and won't leave. They see that the man has a frayed rope around his neck. Audrey sees that the man is shivering and asks to burrow Nathan's jacket. She offers it to him, who hesitantly takes it and puts it on. Suddenly, Forest loses patience, barges in, and orders the officers to quit fooling around and arrest the intruder. The man goes berserk, tears out Forest's throat with his teeth, and escapes.
The EMTs cart away Forest's corpse. Duke and Dwight arrive. Duke asks Dwight if he knows what the Hunter is. Dwight says he doesn't, but warns Duke that if they ever have a rematch, he will make sure none of his blood gets on Duke, making it an even match.
Audrey coordinates a search for the naked man, whose face doesn't appear in any database. As Nathan goes to get a tranquilizer gun, Dr. Claire Callahan comes in and says she is a psychologist assigned to evaluate whether Audrey is of sound mind following her abduction. Audrey brushes her off and says she is fine, but Claire says this is important, Audrey has been through a lot of crazy stuff ever since her arrival in Haven. Nathan sides with Claire, but Audrey is annoyed and refuses to stop working the case.
Nathan and Audrey get a call about the savage from Tor Magnusson and go to his farm. As they talk, Tor's son Liam complains that he can't find his dog Jesse and Tor tells him to go back into the house. They look into the barn and find a dog's corpse, partially eaten, which they figure is Jesse. They look into the trapdoor to the cellar and find dozens of naked men and women sleeping. They tell Tor to lock the barn, but he says that he hasn't kept animals in years so the locks haven't been maintained. Nathan blocks the doors with his truck. Duke calls and says a naked man is raiding the docks and eating the raw fish from some fishing boats. Audrey says they are busy and to handle it himself. Dwight drives up to the docks and Duke lies and says Audrey wanted him to capture the dock savage.
Audrey sees Liam sneak into the barn through a side entrance. The officers go after him and find that the savages have woken up and are putting on old clothing left in the barn. Audrey gets to Liam and they try to hide, but the largest savage sniffs the air and locates them. They get into a room and lock the door, but find another savage inside. However, this one just stares at them innocently like a puppy. Audrey passes him a cookie and he eats it. The large savage tries to break down the door and Nathan shoots him with a taser. The others attack. Nathan shoots one in the leg and the others retreat through the side entrance into the woods, including the large one who recovered quickly.
Tor takes his son back into the house. Nathan gives orders for the savage he shot to have his injuries treated. Audrey shows him the cookie-eating one and says he's different from the others.
Vince stole a copy of Roslyn Toomey's coroner's report. Before her body was burned, she was shot in the back of the head with a bolt gun like the kind used to slaughter cattle.
The cookie-eating savage is put in a jail cell. Audrey gives him more cookies, but can't get him to talk. Claire checks on him and also can't get any response from him. Claire says she wants to come with them for the rest of the case.
They go to the docks. Dwight has trapped the fish-eating savage in his truck, as the savage can't figure out how to open the doors. When Audrey approaches, the savage punches through the glass and tries to grab her. Duke pulls her away and the savage grabs him by the throat, but Dwight punches him out. The savage was cut on the broken glass and his blood gets all over Duke. Nothing happens, and Duke is happy, thinking his Trouble has left him, but the others burst his bubble by suggesting that he only absorbs blood when it is from another Troubled person. Claire gets a call from the hospital saying that the blood of the savage Nathan shot was full of the animal tranquillizer given to dogs before they are put down.
Nathan, Audrey, and Claire head to the Haven Animal Shelter to find the place torn up. A dead naked man is curled up in an impossibly small cage, his neck broken. Horrified, Claire leaves the room to throw up. Audrey notices a frayed rope matching the one around the first savage's neck. She figures that the savages are really transformed dogs, and that the dead man was killed when he transformed while still inside the cage. Claire screams and they run up to find the Shelter's manager, beaten to death with a hammer. They realize the transformed dogs are getting smarter and mastering tool use.
Duke and Dwight visit the Teagues and Dwight says that after he saw how Duke reacted when the savage's blood got on him, he realized that Duke is not like his father. They ask the Teagues to let them look through their archives and Vince reluctantly agrees.
While trying to figure out where the transformed dogs went, the officers find that Tor dropped off Liam's dog Jessie at the Shelter the previous evening. The officers figure that either Tor or Liam are Troubled and head back to the farm. Tor admits that he dropped off Jessie and that the dogs all stopped barking after Tor left. Claire goes to talk to Liam while Audrey warns Tor that he may be Troubled.
While going through the newspapers, a naked man wearing a dog shield runs past the newspaper office. Dwight, Vince, and Dave run out to help, but Duke shrugs and continues reading.
Tor says his grandparents shut down the farm and got rid of all the animals, and Audrey figures that it was to minimize the chances of their Trouble activating. Tor says he dropped off Jesse because he had rabies and had to be put down. Claire reports that Liam has been abducted. Nathan figures that the large savage was Jesse and he wanted Liam. Claire points out that rabies victims become paranoid and that dogs instinctively bury things to protect them.
The group starts a search through the woods, while Claire mildly complains and admits that going through the woods in high heels was a bad idea. The transformed dogs surround them, carrying weapons and working as a pack. Jesse, carrying a gun, advances on them. Tor begs the officers not to shoot Jesse. Claire confirms that Tor feels guilty because he chose to have Jesse put down rather than pay the expensive cost of the shots to cure it.
Claire and Audrey encourage Tor to talk to Jesse. Jesse growls and bares his teeth, but Tor begs Jesse to forgive him for not taking better care of him. He admits that when his wife left him, Liam played with Jesse more than him, and he was jealous. He pats Jesse on the head, and Jesse and the other savages all revert to dog form. The other dogs run off, but Jesse dies. Tor is upset and asks what happened, and Claire sadly explains that humans can survive a rabies infection longer than a dog can, so the human transformation kept him alive. Tor asks how they can find his son without Jesse.
Audrey retrieves the cookie-eating savage, who has reverted to being a dog as well, and uses him to track Liam's scent and locate him. As father and son reunite, Audrey says she doesn't need therapy. Claire lists off some of the past Troubled people Audrey has encountered and says she is the one who helps them heal and readjust to society. Audrey says she wants to adopt the cookie-eating dog. Claire says that's good, and reveals that Nathan was the one who hired her, because he loves Audrey and wants to make sure she is all right.
Later, Dave asks Vince why he cooperated with Duke and Dwight. Vince says somebody already knows their secrets. He points to their file cabinet, which has been broken into with a bolt gun. They figure Audrey's abductor did it.
Duke visits Audrey's apartment and Audrey shows off her new dog, Cookie. Duke is grave serious and reports what he has learned from the newspaper archives. Every 27 years, Haven experiences a meteor shower that is called The Hunter. On that day, the Troubles end. Also, the day it happened in 1956 was the day Sarah disappeared, and the day it happened in 1983 was the day Lucy Ripley disappeared. The next one is in 49 days. Audrey is understandably shocked. Nathan arrives and Duke quickly leaves.
Nathan and Audrey give Cookie to Liam, who happily plays with him. Tor promises that he will love and care for Cookie, because he saved his son. Tor goes to join his family. Nathan asks why she gave the dog away. Instead of telling him what Duke told her, she just says it wouldn't have worked out. They drive off.
- Deleted Scene: Dwight visits the Guns 'n' Roses Diner and greets the waitress, Jordan McKee, who has the circular maze tattoo on her left arm. She asks why he smells like a dog. Dwight says that he hung out with Duke the whole day and has determined that Duke is not a threat. Jordan is upset and says the Crockers cannot be trusted. Dwight protests that Duke is nothing like his ancestors, he wants to help people, not murder them. Jordan glowers and removes her left glove. Terrified, Dwight leaves. Jordan sighs and put her glove back on.