After revealing his true intentions to Audrey and leaving her unconscious in a field, William and his henchmen have been tearing Haven apart by amplifying more and more Troubles. The most recent victim is Doreen, whose Trouble was increased enough to cause a huge fire.
Later that night, Audrey and Nathan try to think of a way to stop William before going to sleep in each other's arms. When Audrey awakes on the floor of a second floor bait shop, she knows that William has struck again.As Audrey walks around town in her pajamas looking for clues, she discovers that she is in an alternate version of the Haven she knows and loves. In this Haven, Duke is a police officer, Nathan is a doctor and Vince and Dave are well-to-do townsfolk. The main difference, however, is that there are no Troubles in this Haven.
Audrey tries to explain her reality to Duke but, as expected, he doesn't believe her. When Vince and Dave turn up dead, Duke throws Audrey in jail and considers her his only lead. The truth is William, who is also stuck in this nicer version of Haven, killed Vince and Dave. William wants things back the way they were and he thinks finding and killing the person with the Trouble who caused the switch will help. Unsure of how to find the right Troubled person, William kidnaps Nathan's family and tells Audrey he'll kill them unless she helps.
Audrey is worried about Nathan's family, but she also knows she can't trust William. Instead, she convinces Nathan to help her find the Troubled person. It doesn't take long for her to find Cliff, the source of this particular Trouble. He wished for a Haven without Troubles and it worked, except that his wife is married to someone else.
Nathan ditches Audrey and takes Cliff to William himself to save his family. True to his word, William lets the family go. Soon, Audrey and a recently-convinced Duke show up to save Cliff but William gets the drop on them. William kills Cliff but not before telling Audrey that he and Audrey actually created the Troubles together as a sick joke.
Once Cliff dies, everything reverts to normal and Audrey fills in Nathan and Duke. Together, they find William but when Nathan shoots William a twin wound appears on Audrey's torso. It seems that Audrey and William really are deeply connected. So, maybe William is telling the truth about her creating the Troubles after all.