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When last we saw Duke he was diving headfirst into the rapidly collapsing barn to save Audrey while Nathan lay dying outside. After Duke experiences what seems like a few seconds of an other-worldly, mind-bending experience inside the barn, he plunges downward and finds himself swimming inside a seal tank in Boston.
Slowly, Duke pieces together that an entire six months have passed and the town of Haven has written him off as dead. Things seem dismal for Duke until Jennifer (a Boston resident who claims she heard Duke, Audrey and Agent Howard talking while they were in the barn) shows up and helps Duke escape from the hospital where he's being held.
After Duke makes contact with Dave (and convinces Dave that he really is still alive), Dave tells Duke how to find Nathan but warns him that Nathan isn't the man he was. Duke sees that for himself when he finds Nathan getting pummeled by bikers … and getting paid for it. Jennifer and Duke watch for a moment and, after a heartfelt reunion, the three of them head back to Haven, despite the fact that Nathan isn't especially welcome there any more.
Once they arrive in Haven, Duke Nathan and Jennifer are quickly confronted by Jordan and the other members of The Guard. The Guard holds them all at gunpoint and it isn't until Nathan convinces them that he's going to end the Troubles for good by letting Audrey kill him that they let him go. Jordan, who is still angry with Nathan for choosing Audrey over her, doesn't trust Nathan to follow it through and is also resentful of Vince's leadership of The Guard.
The one bit of good news is that Dwight has become the town's chief of police in Nathan's absence. He quickly enlists the help of both Nathan and Duke to help him with the increasingly difficult troubles that were supposed to have ended when Audrey went into the barn.
Even though he'd rather go find Audrey, Nathan chips in and helps Dwight track down a woman whose weather Trouble has gone berserk, killing many innocent people in the town. When Nathan finally finds her, he discovers that she and many other people in Haven specifically blame him for the Troubles not ending. Despite that, Nathan convinces her to accept the loss of her husband, which is the event that made her Troubles return. Soon thereafter, she is able to make her peace and disperse the storms she's been causing all over town.
Dwight decides to make it official and offers Nathan a position as a detective. They vow to find Audrey, wherever she is, and help her. Little do they know, Audrey is living a completely new life, working as a bartender named Lexie. As usual, she doesn't remember anything from her past life as Audrey but that might not last since a mysterious man named William shows up at the bar to tell her that unless she remembers who she really is, lots of people will die.