While Nathan and Duke set aside their differences and try to find Audrey, a Troubled individual is plagued by alien abductors.

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.

Audrey and Nathan encounter a bizarre series of deaths suggesting a serial killer, with a unique “trouble”, is at work in Haven. Meanwhile, a Boston cop tries linking the town's latest body to similar cases.

Audrey and Nathan investigate a series of strange incidents where the only common factor is water. Meanwhile, Duke insists on tailing along on the officers' investigation, while the Teagues do some digging on Tommy's background.

A vigilante stalks Haven's criminals, rendering poetic justice. Meanwhile, Nathan grows closer to Jordan as he attempts to infiltrate the Guard, and Audrey learns more about the bolt-gun killer that is stalking her.

On Halloween night, Audrey, Nathan and Duke become trapped inside a haunted house.

While Audrey and Duke track down the Colorado Kid's parents, Nathan and Tommy investigate Troubled incidents involving the resurrection of dead for payment.

A Troubled war veteran sends Duke and Nathan back to 1955. Meanwhile, in the present Audrey tries to deal with an altered timeline where Driscoll's men have taken over the town.

While helping a little girl whose "trouble" is the ability to make people do what she wants Audrey also gathers clues to the identity of the Bolt Gun Killer.

When Haven falls into a deep sleep, Audrey must work with the only other person awake in town. Meanwhile, more questions arise about the Bolt Gun Killer.

Nathan and Duke try to help Audrey search for a troubled killer after a string of murders take place at the Haven High School.

As Audrey grapples with her fate; at the same time she, Nathan and Duke prepare for a showdown with the Bolt Gun Killer.