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.

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.