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.

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.

The residents of Haven have their worst fears come to life while Nathan's "trouble" seems to vanish.

The town's docks start attacking people while the other Audrey Parker probes Audrey's identity crisis.

When a deadly series of electrocutions occur around town, Audrey and Nathan investigate the cause

A wedding at an isolated estate turns deadly for the guests when the site becomes sealed off and something attacks from within.

A single day keeps repeating for Audrey, who finds a deadly accident linked to the phenomenon.

A drowning case exposes a secretive family compound on the outskirts of Haven, from which children have disappeared under mysterious circumstances.

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.

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.

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.

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.