Nathan and Duke - at each others' throats after their brutal fight on Duke's boat - are forced to work together to search for Audrey, who was mysteriously abducted at the end of last season. But their search is impeded by a series of strange events that have some residents worried that Haven is facing something more than just the “usual” supernatural forces – that the town might be ground zero for an alien invasion.
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Audrey, still reeling from her traumatic abduction, feels unsettled about her place in the world - a feeling further complicated when a horde of mindless wild men, who appear to have been abducted, drugged and subjected to strange experiments, begin terrorizing the town. Meanwhile, Duke dives into one of Haven’s greatest unsolved mysteries.
After corpses missing vital organs start popping up around Haven, Audrey and Nathan embark on a manhunt for the most sadistic troubled person they may have ever faced. Meanwhile, Duke must confront the fate his father warned him about: becoming Haven’s curse killer.
A tragic accident causes devastating consequences as Haven is besieged by inexplicable phenomena - a huge wave in the middle of downtown, a shark bite in a community pool, and a drowning inside a shower. The trail of clues leads Audrey and Duke to the rocky coast, as Nathan navigates rough waters himself by meeting with a member of 'The Guard,' a shadowy organization of "troubled" people.
A cold, unstoppable woman is stalking and punishing Haven's criminals, including Duke, who manages to hold his own during a brutal attack. But after Duke discovers that the merciless woman isn't quite as human as she appears, Audrey and Nathan must figure out how to stop her from going too far in the name of justice.
Halloween festivities are put on hold after Audrey and her friends find themselves trapped inside an infamous abandoned house. Audrey searches for a way out, but only finds a way back...in time, to twenty-seven years ago, when she discovers that her past-self Lucy was once trapped within the same house. Meanwhile whatever trapped them in the house begins to put up walls (both literal and figurative) between Nathan and Duke, hoping to drive their tension to the breaking point.
Audrey and Duke head to Colorado to track down more information on "The Colorado Kid." Meanwhile in Haven, Nathan works with Jordan to try to uncover the identity of the Bolt Gun Killer, while he and Tommy investigate a heinous 'troubled' get-rich-quick scheme: someone who can raise the dead - but who kills people and extorts their loved ones for ransom.
Nathan is dead on arrival, literally. Back from Colorado, Audrey and Duke know they only have until sunset to save Nathan's life - but the 'troubled' woman with the resurrection curse is nowhere to be found. In a race against time, an unsuspecting Audrey and Duke team up with Nathan's murderer, learning too late that the man may not be who he says he is...
A trip through time leaves Nathan and Duke stranded in the Haven of 1955. But when Duke and Nathan's actions in the past begin directly affecting present-day Haven, they begin a desperate quest to set things right and find a way back home... and end up crossing paths with Duke's grandfather - a man Duke knows is supposed to be killed by Audrey's alter ego, Sarah.
After finding a burned body in a shallow grave, Audrey is shocked to learn that the corpse is Detective Tommy Bowen, and it's been buried for more than a month... meaning the real Tommy Bowen was dead before they even met him. Meanwhile, the town falls under the spell of a 'troublingly' persuasive seven-year-old girl whose every wish is Haven's command. Nathan digs for answers about the curse only to discover a cold-hearted plot by his 'allies' in The Guard.
Audrey is horrified to discover that Haven's troubled serial killer is a 'skinwalker' - a person who can kill others and wear their skin - and it is still at large. But the investigation is put on hold after Audrey wakes to find all of Haven fast asleep. Finding she isn't alone, Audrey makes fast friends with the only other person left in town.
Haven High's reunion is off to a grisly start when one of the former students turns up dead, forcing Audrey to accompany Nathan and Duke to their reunion when they realize that the corpses piling up are the seventeen-year-old versions of the attending alumni. Meanwhile, Audrey finally uncovers the skinwalker's true identity, and is shocked to learn that the killer they've been hunting all this time has ties the Colorado Kid and Audrey's past life as Lucy Ripley.
With all of the mysteries Audrey has been investigating - the Colorado Kid, the Bolt Gun Killer, The Guard, her own past in Haven - converging at the same place and time, Audrey must face hard truths, and make a terrible decision that will determine the fate of Haven.