Audrey Parker must not only stay on top of Haven's many afflictions, but she must also solve her most challenging case yet: the secret of her own lost past and its ties to Haven. With the help of Nathan Wuornos, a handsome local cop with his own trouble, and Duke Crocker, a local smuggler and reluctant aide in solving Haven's troubles, Audrey digs deeper into uncovering her identity.
The Biblical Plagues of Egypt strike Haven, while Audrey deals with a woman who claims that she is Audrey Parker and Nathan copes with the death of his father. Meanwhile, Reverend Driscoll begins his plan to take control of Haven and eliminate the Troubled.
People start seeing their worst fears, and Nathan and Audrey realize that the visions are tied to the theft of a puzzle board that can destroy Haven. Meanwhile, the new Audrey tries to track down the mysterious FBI Agent Howard and learns of his connection to the late Chief Wournos.
While FBI agent Audrey pursues the investigation into the fake Agent Howard, Nathan and Audrey deal with an outbreak of machines with minds of their own... and a desire to kill.
A mysterious Haven resident may prove the key to helping Nathan and Audrey stop an outbreak of electrocutions. Meanwhile, Duke reluctantly accepts his ex-wife's help finding a way to protect himself from the tattooed man.
Audrey and Duke invite Chris and Evi along to a wedding at an isolated home... and discover that one of the guests is apparently a Troubled individual with the ability to control plant life.
Audrey finds herself trapped by time when a repeating cycle of events involving a runaway car lead to the deaths of her loved ones.
An apparent drowning suicide turns up on a Haven beach, and Audrey and Nathan soon discover that he is tied to an enigmatic family compound, and that the family has abducted a local woman's child. Meanwhile, Duke learns that the family is connected to the tattooed man.
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.
When a Troubled individual unleashes a rotting plague inside the police station, the new Chief orders a quarantine... trapping Audrey and the others inside. Meanwhile, Duke confronts Evi about her betrayal of him.
Audrey and Nathan take a search party into the woods to find a missing boy whose disappearance may be connected to the Troubles, and receive some unwanted help from Driscoll.
With Nathan's help, Audrey finally locates Lucy Ripley and goes to confront her. Meanwhile, Duke and Dwight join forces to discover what Duke's father Simon left for his son.
Haven's dead rise from their graves to reveal the town's secrets... and those of Audrey, Nathan, and Duke.
Audrey is the only one who realizes that there are Christmas decorations in July that no one else finds unusual. The out-of-season decorations are only a prelude to the bizarre bisection of a surfer and a series of escalating disappearances of people who no one can remember except Audrey.