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When "troubles" cleanup man Dwight is arrested by Haven's Officer Stark, he finds out the hard way that Nathan is no longer the chief of police. The new guy in charge is Chief Merrill, a transfer who seems to know nothing about the special needs of Haven. When Officer Stark ends up dead from a strange disease, Audrey and Nathan know it's trouble-related but they can't tell Merrill.
On that same day, Duke brings Evi to the police station so that he and Nathan can interrogate her, but when she shows signs of having the same disease as Officer Stark, Duke must put his plans on hold. Chief Merrill quarantines the entire police station to protect the town from what he thinks is a biological weapon. The only person outside the station that Nathan can trust is Dwight.
Inside the quarantined police station, Chief Merrill contracts the deadly disease and dies while Duke finally gets an explanation from Evi: She was instructed to "help" Duke by getting Nathan fired. Meanwhile, Audrey interviews the people in the station, hoping she can find the "troubled" person causing the disease. When Evi escapes to demand answers on Duke's behalf from the gunmen outside the station, she gets shot and killed.
Nathan barely stops Duke from trying to avenge Evi's death just before Audrey finds the culprit: Nikki Coleman, an abused woman whose fear of her ex-husband is causing the disease. While Audrey talks to Nikki, Dr. Underwood convinces the recently-returned Chris to help him find a gun, but it turns out that Dr. Underwood is Nikki's ex.
Chris tries to use his charm to help, but the only thing that can reverse the disease is Nikki standing up for herself. The more strength she shows, the more the disease retreats from those around her and focuses on her ex-husband. With that problem solved, Nathan must now figure out how to stop the gunmen outside. Just as the gunmen start shooting into the station, Dwight bursts in and saves Nathan with his own "trouble," the power to pull bullets toward him.
With Evi dead, Reverend Driscoll makes a play to control Duke, who pretends to be receptive but isn't; Chris and Audrey break up, with Chris promising to become a better person; and Nathan lets Dwight make Evi's death look like an open and shut case to avoid further investigation. They'll get Reverend Driscoll their own way.