It looks like Audrey Parker #2 is settling in to Haven—she's even helping the other Audrey rent an apartment that Duke owns—but first she wants to check out a mysterious clue she found in the book Special Agent Howard left behind: The latitude and longitude of remote area north of Haven.
When a freak accident at the docks injures a fisherman, Audrey and Nathan are called in to investigate so Audrey #2 decides to investigate Howard's clue on her own. All she needs is Duke to take her up the coast. Duke is none too pleased at the idea but when she offers to hand over an FBI file of his criminal behavior, he can't pass it up.
At the docks, the wounded fisherman is being cared for when suddenly the boat moves by itself again, killing him instantly. The "inanimate" ship is clearly homicidal but who is controlling it? Could it be the very hostile Mr. Halsey who owns the three docks in the area? It looks that way, especially after local repairman Louis Pufahl tells Audrey and Nathan a story about Halsey ignoring the psychic impact of the many people who died aboard that very ship. Unfortunately, it's not just the ship that has become homicidal. Across town, a crane tries to kill a union organizer and almost succeeds.
Meanwhile, Duke and Audrey #2 set sail and discover that they have some common ground in the area of relationships. Audrey confesses her love for a man named Brad whom she hasn't told about the mysteries of Haven yet. When the two of them get to their destination, Audrey #2 finds an abandoned farmhouse and enters it alone. When Nathan finds her much later, she has complete amnesia. Duke suggests they call her boyfriend and Brad promptly shows up to take her away.
She's even forgotten the FBI file that she promised Duke but, no matter, Duke's estranged wife Evidence Brown stole it for him anyway. After the machines kill Mr. Halsey, it gradually becomes clear that the only common denominator is repairman Louis Pufahl—he is the person who has fixed all of these machines. At first, Audrey and Nathan think the machines are acting out his malicious will, but when they discover that the machines have "threatened" Pufahl too, it dawns on them that the machines are attacking anyone threatening to take Pufahl away from Haven and, therefore, away from the machines he nurses back to health.
The machines even try to kill Audrey and Nathan but only succeed in putting a few nails in Nathan's back—lucky for him he can't feel them. Unfortunately, Pufahl's girlfriend Marsha doesn't have the same ability to not feel pain so when an ice machine pins her against a wall, a very panicked Pufahl must save her—by choosing the ice machine over Marsha.