Picking up immediately after the events of last season, Nathan and Duke discover that Audrey's body has been hijacked by Mara. They must thwart her efforts to open another door to the Void while keeping the citizenry of Haven oblivious to the new threat stalking its streets. Their search is complicated when a gory trouble spreads across town and requires their immediate attention.
Nathan and Duke are are coping with the loss of Audrey and Jennifer while Dwight tries to keep Haven together as the chief of police and Mara creates new troubles.
With Mara as his prisoner and The Guard hunting their whereabouts, Nathan flees to a secret hideout where he tries to uncover Audrey's personality buried within Mara. Duke and Dwight must battle a fiery new trouble that threatens to ignite the town. Duke struggles to control his emotions while he grieves for Jennifer, but it seems he is a pressure cooker of troubles…
Nathan and Dwight argue over what to do with Mara; Nathan is convinced Audrey is still alive and he wants to save her but Dwight wants Mara to cure the troubles.
Vince and Dave go to North Carolina to find out more from Dave's secret past but searching may cause a new trouble back in Haven; people are switching bodies.
Nathan and Duke are desperate to get Audrey back so they make a dangerous decision before she's gone for good.
The celebration of Audrey's return is cut short when a supernatural trouble causes Nathan to disappear into a ghostly world. Forced to work alone on solving the trouble, Audrey must also contend with the hostile Guard, who believe she is still Mara. Meanwhile, Duke struggles to accept the dangerous realities of his new condition.
Unable to make headway in her investigation, Audrey recruits an old friend to help her communicate with Nathan, who is still trapped on a ghostly plane. Down in North Carolina, Vince and Dave try to escape the hospital before lab tests on Dave's wound reveal its supernatural origins. Meanwhile, Duke realizes he may have found a kindred spirit in a former foe.
Fearful of exposing the troubles, Nathan, Audrey, and Dwight must hide Haven's sick when a government scientist, Dr. Charlotte Cross, arrives in town. The doctor will not be put off so easily, however, and her investigation raises her suspicions that all is not right in Haven. Meanwhile, Duke contends with feelings of betrayal and considers joining forces with another “outsider.”
As Audrey's health deteriorates, Nathan races to find a cure for the mysterious illness before it is too late. Dwight struggles to contain the contagion but faces interference from Dr. Cross, who has a few secrets up her sleeve as well. Meanwhile, Duke realizes that some old loyalties may be shifting and decides he needs to take matters into his own hands to protect Haven.
As Duke's volatility threatens to unleash unprecedented chaos on Haven, the pressure is on for the CDC doctor to develop a cure for the troubles. Meanwhile, Audrey's symptoms worsen and she must put on a brave face as she and Nathan tackle a psychological trouble, but Nathan grows increasingly worried about her health.
Charlotte makes progress towards developing a cure for the troubles, but it might be too late as Duke's condition takes a turn for the worse. Meanwhile, realizing their objectives may no longer line up, Haven's heroes must reassess where their true loyalties lie.
A game-changing revelation threatens to upend the fragile stability of Haven. Meanwhile, Audrey learns the shocking truth of her origins and must come to terms with her new reality while leading a manhunt to track down Haven's most dangerous enemy before hundreds of new troubles are unleashed upon the unsuspecting town.
New Troubles have infected over half the town and that's the good news.
After revealing her identity as Mara's mother Charlotte informs the gang about the origins of herself and Mara. While Duke continues with his major trouble.
The citizens of Haven put Nathan on trial for his life, and it's up to Dwight and Charlotte to clear his name. Hoping to buy them time, the brothers Teagues moderate the trial as Audrey continues her quest to solve the darkness trouble.
Dwight and Charlotte work on a way to free Audrey from the Sandman's stasis before he can trap her in his mind forever. Duke tries to help Darkside Seeker Seth Byrne recover his memories of Haven.
Charlotte and Audrey start on a plan to stop the troubles.
Nathan tries to track down a terrifying killer; and Duke has a vision of Haven's future.
Nathan and Vince travel back to 1983 to learn the secret of how Croatoan has found a way into Haven. Meanwhile, Duke finds his life on the line when he is apprehended by a mysterious foe.
After entering the Void Nathan encounters an old enemy; Audrey and Duke must stop a new troubled person who is looking for revenge.
Audrey and Duke search for a way to save Nathan from the Void. Dave must plumb the depths of his own mind in his struggle to free himself from Croatoan's deadly grasp.
Audrey and Nathan try to regain control of the police station while a mysterious killer leaves a wake of bodies.
Nathan and Dwight race to rescue Audrey from Croatoan, but the consequences of Duke's dark destiny wreak havoc on their plans. Meanwhile, Vince contemplates an unusual sacrifice.
Haven's heroes struggle to rebuild the Barn in the face of mounting obstacles. Dwight is tempted by a surprise gift and Nathan must consider a devastating sacrifice.
Nathan struggles to return to Haven; Dwight reconsiders his future; Audrey realizes the way she can save the town from Croatoan.