'Haven' starts of this episode with the last 30 seconds of the previous episode. The barn appears and out steps Agent Howard with James Cogan. James runs off into the night.
Duke and Nathan are searching for Audrey who has been captured by Arla. Arla and Audrey stumble upon Agent Howard who tells them that James is in town and unaware that 27 years have passed. Arla goes off to find James and Agent Howard explains to Audrey that he and the barn both appear when she is ready. That for the Troubles to stop she has to willingly enter the barn. There is a catch, of course. If Audrey doesn't enter the barn then the entire town and everyone in it will be destroyed by meteors.
Audrey hears someone coming and turns to find Nathan and Duke approaching. Agent Howard and the barn have both vanished. Audrey fills the guys in on what is going on and they race to find James and figure out a way to stop the Troubles and keep her from leaving.
Arla finds James and the two reunite. He questions why she still looks so young and she says that she didn't age for him. He's sick and growing more ill by the minute. Apparently the barn was the only thing keeping him alive. Duke calls Arla and tells her that Audrey will not leave without James and will summon the barn to save him. Duke admits that Audrey has to enter the barn and tells Arla to meet him and he will take care of the rest.
Audrey and Nathan arrive at the barn to find Duke, Arla and James. Arla holds them at gunpoint and Duke reveals that the gun is empty; he removed the bullets. Audrey goes to James and decides to take him into the barn to save him, figuring that it won't leave until she tells it to do so. James recovers enough to run into the barn on his own. Audrey decides to go after him and both Nathan and Duke want ot go with her. Nathan goes and Duke stays to guard Arla.
Inside the barn, Nathan and Audrey decide to destroy it and they suddenly find themselves back in 1953 and outside the barn. They see Sarah, Vince and Dave attempting to destroy the barn. It has no impact. Sarah says she has to go and the brothers ask about the baby. She says that he is someplace safe. When Dave asks if the boy is with his father Sarah smiles and says that his father hasn't even been born yet. Immediately after that Audrey and Nathan are back inside the barn in the present with Agent Howard. When they question the validity of the memory Agent Howard shows them one Nathan recognizes. It's of him and Sarah having sex. He is the father of her child.
Nathan admits that he slept with Sarah as a way of being with Audrey and because he didn't think he was going to be able to get back to her in the present. Audrey is pleased that he is the father of her son and that there is some tangible proof that she exists. They split up to try to find James.
Nathan finds James and they talk with Nathan revealing his identity. James doesn't have any more answers than Audrey, really. He says that Audrey has to kill someone she loves to break the cycle. James believes that she wants to kill him and runs off when she appears.
Audrey calls to Agent Howard and says she will not make her choice until she sees James. James reappears and demands to see Arla. Audrey goes to get her and when she enters the barn her Trouble stops and her identity as a skinwalker becomes apparent. Arla takes out a knife and tries to kill Audrey but James gets in the way and she stabs him instead. Arla and Audrey struggle over the knife and Arla is killed.
Meanwhile, outside the barn Duke is pacing and waiting to see what will happen when the Guard shows up. They have something of a standoff with Jordan and the others until Vince arrives and sends them home. It seems that he's the head of the Guard and the reason they never bother Duke.
Back in the barn, Audrey tells Nathan to take the skinwalker outside. She turns and James is gone. Agent Howard says that he is part of the barn and now healing from his injuries. Audrey why she has to go and Agent Howard says that every 27 years the barn needs a recharge. She charges back up and then it vanishes, keeping the Troubles at bay. She has no real choice in the matter. Audrey agrees with Agent Howard and says that she has to go and say goodbye to her friends.
Outside she says goodbye to Vince, Dave and Dwight. She kisses Duke on the cheek and then hugs Nathan, stealing his gun. He refuses to let her go and she gives the gun to Duke making him promise to keep Nathan out of the barn. Audrey enters the barn.
Nathan tries to go after her, grabbing the gun from Duke. When he realizes that he can't harm the barn he turns the gun on Agent Howard. Jordan appears and shoots him. Not being able to feel pain, Nathan fires at Agent Howard. As he does so the barn and Howard both begin to shatter into beams of light. Nathan collapses and as the barn is vanishing into the light Duke jumps in after her.
'Haven' ends with Nathan looking up at the sky as meteors fall all around him.