FBI Agent Audrey Parker goes to the small town of Haven, Maine, to track down an escaped prisoner. When he turns up dead, the local authorities are ready to dismiss it as a freak accident. However, the bizarre circumstances of the death, strange storms, and spreading cracks in the ground make Audrey think there's more to Haven than meets the eye. With the aid of local police officer Nathan Wuornos, Audrey vows to find out how the prisoner really died.
Butterflies are a foreshadowing of doom when they appear at the scenes of several bizarre events, all of which target a hostile reverend, his daughter, and her foster son. Meanwhile, Audrey stays in Haven to determine the identity of her lookalike in the Colorado Kid murder photo.
A doctor at a psychiatric facility inadvertently exposes himself to a drug that causes him to go temporarily insane, but seemingly cures three patients. Audrey and Nathan help recover the patients. When all of the afflicted revert to their original mental states, they realize that something more is going on.
Audrey and Nathan look into an epidemic that threatens the town's livestock and fields, and is centered around two brothers and their complicated relationship. Meanwhile, the Teagues brother offer Audrey some fashion tips.
Two men turn up dead, the victims of accelerated aging and decomposition. Nathan and Audrey trace the dead men and discover that their common connection is that they were both at the Grey Gull, Duke Crocker's new bar... and Duke is the next target.
Local hunt club members are the victims of wild animal attacks, but Emily and Nathan soon realize that a Troubled human is responsible
A woman manifests the Troubled ability to make whatever she sketches become real.
When two medical staff members at a cancer clinic are killed, stabbed through the heart, Audrey and Nathan investigate and realize that a shadow creature, a "Dark Man," is responsible.
Audrey's new Haven friends surprise her at an isolated local hotel and give her a birthday party. However, they soon discover that their host is a chameleon, a shapeshifter influenced by the Troubles to start killing and taking on new forms. Soon no one knows who is who, or who can be trusted.
While Audrey investigates Duke's connection to the Colorado Kid, she comes across a high school guidance counselor who appears to be responsible for the fiery deaths of two people. However, the counselor insists that she tried to prevent the deaths... and there are more to come.
Two crooks hijack Duke's ship in an attempt to locate a smuggled box, and end up capturing Audrey, her visiting boss, Duke, and Julia.
A dead man's family is scorned for the death of the crew he killed in a boating accident, and their house is plagued by strange phenomenon. While Audrey investigates the home, Nathan is forced to pose as a criminal to convince Duke to share what he knows about the accident.
A former Haven resident returns and wants the life that he claims Chief Wournos took from him. Meanwhile, more cracks spread throughout Haven, Audrey realizes who she really is, Nathan learns the truth about his father, and Duke and Julia pursue the mystery of the tattooed killers.
In the aftermath of Chief Wournos' death, Nathan and Audrey deal with a woman claiming to be Audrey, the ten Plagues of Egypt, and Reverend Driscoll's attempts to take control of Haven.
A girl who can project a person's worse fear sets off a panic in Haven. As Nathan and Audrey investigate, they discover that another Troubled person is involved, one who needs the woman's affliction... and Nathan's. Meanwhile, Audrey Two tries to track down Audrey's Agent Howard.
Machines come to life and start killing people in Haven. While Audrey and Nathan try to deal with the new crisis, Audrey Two investigates the mystery of Agent Howard.
A Troubled individual with electrical powers threatens the entire town. Meanwhile, Duke tries to find the secret that will let him ward off his tattooed killer.
The children of two feuding families attempt to marry. However, their wedding is disrupted when the plant life animates and attacks everyone... including Audrey, Chris, Duke, and Evi. Meanwhile, Nathan tries to come to terms with Audrey's new relationship with Chris.
Audrey discovers that the same five hours keep repeating over and over... and each time before resetting, someone close to her dies in a car accident.
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 straight-laced banker hides a double life... literally. Meanwhile, Driscoll continues his plan to remove Nathan from office and Duke helps a runaway.
An unidentified Troubled individual unleashes a virulent plague in the station house. The new chief of police orders a quarantine, trapping Audrey, Nathan, Duke, Evi, and Chris inside.
A teen seemingly dies at the hands of a serial killer, but an investigation soon reveals that the killer is dead and the teen may be Troubled. Nathan and Audrey search the woods for the boy, but soon discover they have unwanted assistance from Driscoll... and Duke Crocker.
Two mummification deaths increase the town's tensions in the aftermath of Audrey's shooting of Reverend Driscoll. While Nathan decides which side he will support, the Troubled or the unafflicted, Audrey finally locates Lucy Ripley and Duke joins forces with Dwight to learn his father's secrets.
As the civil war between normals and Troubled in Haven comes to a head, Nathan and Duke are visited by the ghosts of their fathers... and Reverend Driscoll, who plans to eliminate the Troubled once and for all with the help of someone close to Audrey.
After a surfer is cut in half in the middle of the harbor, Audrey soon realizes that everyone is celebrating Christmas... in July, with no idea that anything unusual is going on. Things become more sinister when people disappear and no one but Audrey can remember they ever existed.