Haven is a mysterious town where supernatural afflictions, known as "Troubles," regularly manifest, causing chaos and danger. FBI agent Audrey Parker arrives in Haven and soon discovers she has a deep, unexplained connection to the town and its recurring Troubles. She partners with local detective Nathan Wuornos, who is immune to the Troubles, and often finds herself at odds with Duke Crocker, a charming smuggler whose family lineage is cursed by the Troubles. Audrey's primary goal is to understand her true identity and the mystery of the "Colorado Kid," a figure from her past, while also trying to stop the Troubles from destroying Haven.

This season, Audrey learns a shocking truth: she is a recurring figure who appears in Haven every 27 years to stop the Troubles, only to disappear when a celestial event called the "Hunter" occurs. The search for the Colorado Kid intensifies when his grave is found to be empty, suggesting he may still be alive. A new threat emerges in the form of the "Bolt Gun Killer," who targets Troubled individuals. Nathan and Duke are unexpectedly sent back to 1955, where Nathan falls for "Sarah," an earlier identity of Audrey. Later, the Bolt Gun Killer is revealed to be a skin-walker named Arla Cogan, the Colorado Kid's wife, who manipulates events to force Audrey into a mysterious barn.

As the season culminates, Audrey faces an impossible choice. To end the cycle of Troubles plaguing Haven, she must enter the barn, a sacrifice that means her disappearance. Audrey enters the barn, seemingly sacrificing herself to stop the Troubles, and Duke disappears into the barn as it vanishes. Haven is left facing destruction from an impending meteor storm, leaving Nathan alone amidst the chaos.

Season 3 of Haven covers episodes 1-13. Here's everything that happened:

Season 3, Episode 1: 301 - Audrey is held captive by a mysterious man demanding information about the Colorado Kid. Meanwhile, Haven is plagued by bizarre alien phenomena, and Nathan and Duke's conflict escalates. The Colorado Kid's grave is found to be empty, and Audrey discovers a cryptic message in her own handwriting from 27 years prior, hinting that the Colorado Kid may still be alive.

Season 3, Episode 2: Stay - A mysterious affliction causes people to transform into naked, growling men. Audrey and Nathan investigate, discovering the transformations are linked to a farmer's dog. The episode reveals that the "Hunter" is a meteor storm that occurs every 27 years, and Audrey's past personas disappear during it. Audrey learns she has only two months until the next storm.

Season 3, Episode 3: The Farmer - A series of gruesome murders, where victims have their organs removed, leads Audrey and Nathan to a troubled individual from a local fertility clinic. This individual's "Trouble" causes his organs to fail, forcing him to harvest them from family members. Duke is forced to kill the troubled man, ending the cycle of organ harvesting. Meanwhile, Audrey grapples with her impending disappearance due to the Hunter meteor shower.

Season 3, Episode 4: Over My Head - As mysterious drownings plague Haven, Audrey investigates a series of ocean-related deaths, suspecting a connection to the elusive Bolt Gun Killer. Meanwhile, Audrey experiences a powerful flashback to the day the Colorado Kid died, triggered by her locket. The episode concludes with Audrey and Duke working to locate Daphne, who is trapped in a car as the tide rises, and Audrey realizing Daphne might be the link between the victims.

Season 3, Episode 5: Double Jeopardy - A mysterious woman in white begins brutally attacking criminals in Haven. Duke Crocker is targeted, and Audrey suspects this "woman in white" is connected to other recent violent crimes. The episode concludes with the revelation that the attacker is a Troubled individual who can shatter into plaster when harmed, and the bolt-gun killer is shown sewing body parts, implying a horrifying new creation.

Season 3, Episode 6: Real Estate - Lured to a notorious haunted house on Halloween, Audrey, Nathan, Duke, and others become trapped. The house's malevolent spirit, Roland Holloway, forces them to confront their fears and each other. Chad is found dead, and later, Tina is impaled, as the house manipulates events, ultimately leading to its destruction by bomb.

Season 3, Episode 7: Magic Hour (1) - While Audrey and Duke investigate the parents of the Colorado Kid in Colorado, Nathan and Tommy deal with a "trouble" in Haven where the dead are being resurrected for payment. Rica Hamilton is killed by a car, only to be miraculously revived, but then Noelle is shot and killed by Tommy. The episode ends with Audrey finding Nathan seemingly dead.

Season 3, Episode 8: Magic Hour (2) - Audrey and Duke team up with the killer they've been hunting to save Nathan, who is in critical condition. They race to find a woman with the power to resurrect the dead. Meanwhile, the Teagues discover the Bolt Gun Killer has manipulated them and track the murderer to his true target. The episode concludes with Nathan's life hanging in the balance as they desperately seek the resurrection touch.

Season 3, Episode 9: Sarah - Duke and Nathan are sent back to 1955, where Duke's actions to save his grandfather inadvertently alter the timeline. In the past, Nathan develops feelings for Sarah, an earlier identity of Audrey. The episode concludes with Sarah killing Duke's grandfather in self-defense, and Audrey realizing the dire consequences of their temporal meddling.

Season 3, Episode 10: Burned - Audrey and Nathan investigate a burned body, only to discover it's Tommy, but the real Tommy died weeks ago. They encounter Ginger, a girl with mind-control abilities, who reveals the Guard's manipulative intentions. The Bolt Gun Killer is revealed to be a skin-walker, and Jordan attempts to kidnap Ginger, leading to her arrest. The episode concludes with Audrey realizing she must enter the barn to end the Troubles.

Season 3, Episode 11: Last Goodbyes - Audrey awakens to find all of Haven in a deep sleep, except for a man suffering from amnesia. She discovers he inadvertently caused the town-wide coma when his fear of dying triggered his Trouble. To save everyone, he must be returned to his coma, leading to his sacrifice to end the mass unconsciousness. The episode also reveals Claire Callahan was a skin used by the Bolt Gun Killer.

Season 3, Episode 12: Reunion - A killer targets attendees at Nathan's high school reunion, reverting them to their teenage selves before murdering them. The Skinwalker is revealed to be Arla Cogan, the Colorado Kid's wife, who seeks Audrey's help to reach the barn. Arla's true identity and motive are exposed, and she is apprehended by the Teague brothers. The episode concludes with Audrey facing the impending arrival of the barn.

Season 3, Episode 13: Thanks for the Memories - As a meteor storm threatens Haven, Audrey, Nathan, and Duke confront the Bolt Gun Killer and Audrey's impending fate. James Cogan, revealed to be Nathan's son with Sarah, is brought to the barn by Arla. Audrey enters the barn, sacrificing herself to end the Troubles, and Duke disappears into the barn as it vanishes. The episode concludes with Haven facing destruction from the meteor storm, leaving Nathan alone.