When FBI Special Agent Audrey Parker is dispatched to the small town of Haven, Maine, on a routine case, she soon finds herself increasingly involved in the return of "The Troubles", a plague of supernatural afflictions that have occurred in the town at least twice before. With an openness to the possibility of the paranormal, she also finds a more personal link in Haven that may lead her to the mother she has never known.

She and her partner, police detective Nathan Wuornos, find themselves frequently facing problems caused by both the effects of the Troubles, as well as the activities of town folk who take more drastic measures against those who are Troubled.