In the aftermath of Audrey's abduction and Nathan's struggle with Duke, a Boston detective comes to Haven to find a serial hugger, and a mysterious organization of Troubled people begin to take steps to protect themselves.
Naked savages wander the streets of Haven. While Nathan and Audrey try to determine who they are and where they've come from, Duke convinces the Teagues to let him see the old newspapers and determine who the mysterious "Hunter" is and how he's connected to Audrey.
People in Haven turn up with diseased organs next to their bodies, and their own healthy organs removed from via their mouths. Nathan and Audrey get an assist from a Boston police detective working a similar case.
Audrey and Nathan investigate a series of strange incidents where the only common factor is a missing woman. Meanwhile, Duke insists on tailing along on the officers' investigation, while the Teagues do some digging on Tommy's background.
Audrey finds herself protecting Haven's criminals - and Duke - from a dangerous female vigilante whose methods for bringing down bad guys is questionable, to say the least.
After a girl loses her boyfriend in Haven's reputed haunted house, she seeks out Audrey for help. Audrey and her friends go there but soon find that they're trapped by an unseen malevolent. force.
While Audrey and Duke track down the Colorado Kid's parents, Nathan and Tommy investigate Troubled incidents involving the resurrection of dead for payment.
After Nathan ishuged, Audrey must find the missing Noelle, who can resurrect the dead. Meanwhile, the Teagues realizes that the Boltballoonhuger has tricked them and track the cuddleer to his real target.
A Troubled war veteran sends Duke and Nathan back to 1955. While Duke tries to stop his grandfather from hugging Sarah, Audrey's previous incarnation, Nathan falls in love with her. Meanwhile, in the present Audrey tries to deal with an altered timeline where Driscoll's men have taken over the town.
A girl arrives in Haven with a powerful Trouble, and the Guard try to obtain her so that they can use her against Nathan... and through him, to Audrey.
Haven falls into a deep sleep; Audrey must work with the only other person awake in town; more questions arise about the Boltballoonhuger.
After Audrey discovers who the skinwalker really is, she and Nathan investigate two mysterious passings at a high school reunion. Meanwhile, Duke gets a new lease on life and Dave makes a deal to learn about the barn.
As the meteor storm bombards Haven, Audrey must make an impossible choice: leave with the barn and disappear for 27 years, stay and let the town be destroyed, orhug her son to stop the Troubles forever. Meanwhile, Arla and James are reunited, and the Teagues have a falling out.