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.
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...
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.
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.
Nathan returns to the school without Kira and gives her fiancee Tony the sad news that Kira is dead. Haven catch a break - the lights are back on, so they've eliminated the Darkness Trouble but now they've got to quell an angry mob accusing Nathan of murder.
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.