The next morning, Duke and Nathan arrive at the Grey Gull and discover that someone has killed the man Duke had watching Audrey. Duke figures that Arla killed his man and is now looking for the barn with Audrey. When they wonder if Arla has already found the barn, Duke says that the Troubles would be gone if she had. Nathan slaps him, angry that Duke has apparently forgotten Audrey. However, Duke explains that he only meant that as long as Nathan has his Trouble then it means that Arla hasn't succeeded yet. They remember that the barn left an imprint at Kick'em Jenny Neck and prepare to take a boat there... only to discover that Arla has stolen Duke's boat.
Arla takes Audrey to the field and find Agent Howard watching birds. He offers to take Audrey to the barn and tells Arla that her husband James went to the bakery in Haven, and that he has no idea that 27 years have passed since Lucy took him into the barn. Howard calls James on the cell phone that he gave him and hands his phone to Arla, who tells James that she'll be there. She tells Audrey to stay there and heads into town, and Howard leads Audrey to the barn.
As they approach the spot, Howard stops at his camp and pours tea for Audrey. He explains that he dropped Audrey off 27 years ago and has returned to pick her up. The barn appears and Howard explains that it appears when Audrey is ready for it. However, the agent explains that he can't force Audrey into it: she has to enter it of her own free will or the Troubles won't end. When Audrey says that she doesn't want to leave and "die" again, Howard admits that it will likely happen. However, he suggests that she go off and find a way to stay. However, Howard warns her that the meteors will come down and destroy Haven unless she enters the barn.
Duke and Nathan arrive, having stolen a boat to get there. When Audrey tries to explain, she discovers that Howard and the barn have both disappeared. She decides to find Arla and James, remembering that Arla said her husband knew of another way to stop the Troubles. As they head toward Haven, the Hunter meteor shower begins, hitting the town.
Dwight finds Vince outside of the Herald, loading up his car. When Dwight asks to borrow a jack, he hears a noise from the trunk and Vince reluctantly opens it. Dave, bound and gagged, is inside. Vince explains that his brother attacked him and then released the captive Arla. Dwight says that it's too dangerous to leave Dave in the trunk now that the meteor storm has begun, and Vince reluctantly agrees. However, as soon as the cleaner leaves, Vince slams the trunk shut and keeps packing.
Audrey and the others go to the bakery and discover that James and Arla have already gone. A waiter tells them that James appeared sick and Nathan figures that the barn was keeping James alive. Duke says that he'll go to the dock to check the security footage while Nathan and Audrey put out an APB on the couple.
Arla takes the ailing James to the boarding house room she's using and tries to tend to him. He wonders why she hasn't aged in 27 years but she simply keeps tending him. When he asks about his mother, Arla insists that she won't lose him again. As they talk, Duke calls Arla on her cell phone and she takes the call privately. Duke tells her that Audrey won't go into the barn until she knows James is safe, and suggests that Audrey will summon the barn to save James. He tells Arla to bring James to the barn and meet him there, and he'll take care of the rest.
Dwight goes back to Vince's car and finds Dave is still in the trunk. He lets Dave out and the newspaperman explains that Vince tied him up because they disagreed on what to do about Audrey. Vince wants Audrey to end the Troubles by entering the barn but Dave is sick of using Sarah/Lucy/Audrey as a 27-year stop-gap. Fifty-four years ago they tried to keep Sarah out of the barn and it didn't work. Dave figures that they need to find Vince and assures Dwight that he knows where his brother is going.
Arla meets Duke in the woods and together they take James to the barn. When Duke wonders why she's murdered, Arla insists that she's doing it for love and pointedly tells Duke that if he were ever in love then he'd understand. As they get to the barn, Audrey and Nathan arrive and Arla threatens them with her gun. She tells Audrey to take James into the barn so he can be healed again and then to bring him out. Audrey refuses and Arla prepares to shoot Nathan as a threat. However, Duke steps forward and explains that he removed the bullets, just as he did when Arla was disguised as Tommy. He takes the gun from Arla and tells her that he does want the Troubles to stay, but he doesn't to lose Audrey to do it. As Audrey checks on her dying son, Arla begs her to take James into the barn before it disappears. However, Audrey figures that since the barn is responsive to her, it won't leave until she wants it to leave, with or without her.
As they talk, James manages to slip away and enters the barn. Audrey prepares to go after him, and Duke reluctantly stays behind to guard Arla while Nathan goes with Audrey. As Nathan starts to go in, Duke stops him long enough to make him promise to bring Audrey out again. The two officers steps through the doors and find themselves in a featureless white hallway filled with doors that lead into other hallways. Nathan realizes that he can feel and they realize the barn negates the Troubles. He suggests that they destroy the barn and end the Troubles...
... and Nathan and Audrey find themselves outside the barn. Fifty-four year younger versions of Dave and Vince drive up with Sarah. They can't see Audrey and Nathan, and the brothers place dynamite and try to blow up the barn. The explosion has no effect and Sarah says that she has to go into the bar. She thanks them for taking her infant son James somewhere safe and tells them that James' father hasn't been born. As Audrey tries to work out what her other self means, Nathan realizes that Sarah is referring to him.
Agent Howard emerges from the barn to confront Nathan and Audrey, who find themselves back in the same corridor. He explains that he showed them some of Sarah's memories, but Nathan isn't convinced they were real. To prove what he's saying, Howard shows them a memory that Nathan is true. Nathan and Audrey find themselves on a beach in 1955. Audrey looks around despite Nathan's efforts and finds him in a parked car... with Sarah, making love. The barn appears nearby and the modern-day James comes out, sees Nathan and Audrey, and goes back inside.
Nathan and Audrey go through the doors after him and Nathan finds himself alone in a corridor. James comes out and Nathan explains that he's his father. When he tries to assure James that Audrey is trying to help, he insists that Audrey plan to kill him. James explains that when he came to Haven in 1985 to find his mother Sarah, he discovered Lucy instead. She was getting ready to enter the barn to end the Troubles and James discovered that if she killed him, it would also end the Troubles. Before he could get to Lucy, someone attacked him from behind on the beach in 1985. As they talk, Audrey comes up and James leaves before she can see him.
Outside, Arla and Duke wait and Arla realizes that Duke is in love with Audrey. He denies it just as Kate and the Guard arrive. Kate assures Duke that they don't want him dead and are satisfied that Audrey is in the barn, just as they want. They plan to make sure that Audrey doesn't leave and stop the Troubles from ending for 276 years. When Kate points out that Duke will be free of his curse, Arla explains that Duke is in love with Audrey and Kate warns him that neither he nor Nathan can have Audrey.
Nathan tells Audrey that James is his son and Sarah's, and that he made love to Sarah in 1958 because he couldn't have Audrey. Audrey admits that she's happy it happened because at least there will be something of her left behind when she disappears. Nathan promises that she won't disappear and tells her what James told him about ending the Troubles with his death. Audrey calls for Howard, saying that she won't make a choice until she sees James. Howard and James appear, but James demands to see Arla and punches Nathan. Realizing she won't get his cooperation otherwise, Audrey goes to get Arla.
David is running through the woods when Vince shoots him with a tranquilizer dart. However, it's a trap: Dwight grabs Vince and Dave reveals he's wearing a bulletproof vest. Vince insists that Audrey has to enter the barn and stop the Troubles, but Dave refuses to keep using her and wants to give her a chance to find an alternative. They go to the barn and Vince steps forward, revealing his Guard tattoo. He orders Kirk and the others to leave and they obey. Kate, unaware of who was running the Guard, is surprised to learn that Vince is in charge. Vince tells her that Audrey will get the chance to make her own decision and she reluctantly leaves. Meanwhile, Vince tells Duke that his orders are the only reason that the Guard didn't try to kill the smuggler and fulfill Duke's death prophecy.
Audrey comes out of the barn and tells Arla that her husband wants to see her. However, when Arla goes in and hugs her husband, the barn stops her Trouble... and her skin starts falling off. As James stares in horror, Arla explains that her Troubles were set off by his death. Audrey tells her son that Arla has been murdering women to regain her face for him and a disgusted James shoves her away. Furious, Arla draws a knife and lunges at Audrey, but James tries to stab her and takes the blow intended for his mother. Audrey wrestles with Arla and the skinwalker falls on her own knife.
Audrey emerges from the barn and tells Arla that James wants to see her. She goes into the barn and hugs James, but her Trouble stops because of the barn's effects. Her skin starts falling apart and Arla explains that her Troubles started when he died. Audrey says that Arla has murdered women to take their skin and James shoves her away, disgusted. Furious, Arla draws a knife and tries to kill Audrey, but James tries to stop her and she stabs him instead. When Audrey tries to stop her, they struggle and Arla falls on the knife. While Nathan takes Arla out of the barn, Audrey goes to her son and he explains that Arla must have lied to him about Lucy killing him. He tells Audrey that Lucy was the one who told him that her killing someone she loves would stop the Troubles for good. Since Audrey doesn't love him because she doesn't know him, she can't kill him to stop the Troubles. He asks her who she does love.
Howard returns and asks Audrey if she's ready to leave. James disappears and Howard explains that since he's part of the barn like Audrey, he will heal. When Audrey wonders what is happening, Howard explains that as long as she is in the barn, Audrey's energies stop the Troubles. However, every 27 years the energies wear out and Audrey and her predecessors become a new person and then come out to recharge with love. Audrey wonders if someone or something is punishing her and Howard admits that it seems that way. He then warns her that now that she knows the second way to stop the Troubles, she must choose as those are her only two options.
Before she goes, Audrey says that she has to say goodbye to her friends. She goes out with Howard and Audrey explains to them that she must kill someone she loves to stop the Troubles. She thanks Dwight and the Teagues, and then says goodbye to Duke, saying that she particularly appreciated their time together in Colorado. Audrey kisses Duke on the cheek and then goes to Nathan and kisses him on the mouth. Nathan would rather than die than let her go and Audrey, well aware of his feelings, gives her gun to Duke and asks him to make sure Nathan doesn't follow her. Duke takes the gun and promises to hold Nathan at bay, and Audrey jokes that they'll get to do it again in 27 years. When Nathan tries to push past Duke, the smuggler says that they have to let Audrey choose, even though they both hate it.
As Audrey goes back into the barn, Nathan realizes that Duke loves Audrey as well. he wonders how Duke can let her go and yanks the gun away, but Audrey goes in and closes the door. Nathan tries to open it without success, and then turns and aims the gun at Howard. Before he can shoot, Kate comes back and shoots Nathan in the back. As he collapses, Nathan shoots Howard repeatedly and Duke grabs Nathan's gun and shoots Kate.
The barn starts to implode, emitting light in all directions. Howard's corpse does the same thing and disappears in a burst of white light. Arla is sucked into the barn and Nathan tells Duke to save Audrey. Duke yells to Audrey and jumps into the barn just as it disappears, leaving Nathan alone in the middle of the field as the meteors slam down into Haven.