FBI agent Audrey Parker travels to the town of Haven to investigate the death of an escaped prisoner who fled to his hometown. She soon discovers the man's death is merely the tip of a very large iceberg of supernatural phenomena.

Audrey and Nathan learn of a ghost story that wanders the Haven clinic and takes the lives of sick people before their time.

As the mysterious cracks spread throughout Haven at an increasing rate, a mysterious criminal returns to Haven and Audrey discovers the secrets of her past and her mother's.

Haven is beset by biblical plagues. Duke continues looking for information on the tattoo, with a little help from his past. Audrey and Nathan check out Audrey II, and try to figure out what to do about Chief Wuornos.

A banker hides a dark secret that connects him to a killer hiding in Haven. Meanwhile, Duke helps a young runaway and Nathan discovers that his job is at risk.

Haven's dead rise from their graves to reveal the town's secrets... and those of Audrey, Nathan, and Duke.

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 Duke return from Colorado. Audrey, Duke and Tommy try to find the woman with the resurrection touch. Meanwhile, the Teagues realizes that the Bolt Gun Killer has tricked them and track the murderer to his real target.

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

Nathan and Vince travel back to the year 1983 in order to discover Croatoan's origins in Haven; at the same time, Duke finds himself in grave danger after being apprehended by a mysterious foe.