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 remains in Haven to investigate her mother's connection to the Colorado Kid, but ends up working with Nathan to determine the cause of a mysterious series of incidents that involve butterflies and otherworldly phenomena centered on a angry reverend, his passive daughter, and her foster son.

A plague of insanity strikes at a local hospital, causing the doctors to go insane... and the patients to become normal. Audrey and Nathan seek to discover the cause before it spreads further.

Haven is stricken by a mysterious plague when animals and plants alike are destroyed by exposure to hydrochloric acid with no discernible source.

Young men in Haven start aging at an accelerated rate, and Audrey and Nathan attempt to find the source.

A series of fatal animal attacks lead Audrey and Nathan to investigate a local woman who supports animal rights. However, they soon discover that while she may not be Troubled, the person responsible is... and Chief Wournos is the next target.

Two mysterious assaults involve crooked businessmen, and sketching charcoal is found at each crime scene. However, the boy the officers suspect is responsible becomes a third victim, leaving them to pursue a new line of investigation.

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

Audrey's surprise birthday party at a local hotel goes awry when a shapeshifter stalks the partygoers, and nobody knows who can be trusted.

Nathan and Audrey investigate a series of murders, but the prime suspect insists that she's trying to stop the real killer. Meanwhile, in the aftermath of Duke's revelation, Audrey continues to investigate the Colorado Kid mystery involving her mother.

Audrey joins in a friendly game of poker aboard Duke's ship, but the two new players soon lock everyone up and try to find a box that Duke is smuggling. Meanwhile, Audrey's boss arrives in town and demands answers.

Audrey and Nathan investigate when a gust of wind seemingly throws a woman into a wall following an argument, and the FBI agent suspects some children may have telekinetic powers.

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.

Nathan, Duke, and Lexie find themselves in a race against time to find the troubled person responsible for turning people hard as stone.

Nathan and Lexie hunt a trouble that attacks Haven's citizens in their nightmares; Duke deals with the nightmare his brother has become.

Audrey, Nathan and Duke's victory over William feels hollow as they deal with the aftermath of Duke on death's door, Mara in control of Audrey's body, and a strange trouble supernaturally silencing citizens all over town.

Duke struggles to accept Jennifer's death; Nathan searches for some shred of Audrey in Mara's cruel personality; Dwight shoulders the heavy burden of holding Haven together.

When Vince and Dave travel to North Carolina, their probing of Dave's past uncovers a body-swapping problem back in Haven.

When Audrey and dozens of Haven citizens are affected by a mysterious illness, the symptoms threaten to expose Haven’s secrets to a dangerous newcomer.

As Mara'a endgame becomes clear, Nathan and Audrey pursue a plan to stop her once and for all.

Nathan receives otherworldly help as he works to track down a terrifying killer; and Duke reaches a crossroads after he has an alarming vision of Haven's future.

Hope of ending the troubles begins to fade as the heroes struggle to rebuild the Barn in the face of mounting obstacles. And while Dwight is tempted by a surprise gift, Nathan finds himself considering a devastating sacrifice.

Nathan struggles to return to Haven as Dwight reconsiders his future in the series finale, which also finds Audrey coming to a terrifying decision about how she might finally save the town from Croatoan.