Audrey is missing and Nathan is furious. He barges onto Duke's boat and accuses Duke of abducting Audrey. Duke denies any wrongdoing and tries to fight Nathan off, especially since he sees that Nathan now bears the tattoo of the person who is fated to kill him.
The two of them tussle, each of them almost killing the other until everything made of metal suddenly flies to the ceiling of the boat. After the interruption, Duke and Nathan mend fences, at least long enough to begin a joint search for Audrey.
In town, the two of them discover that the whole town was affected by the same metal magnetism that they experienced and Dwight is busy spinning a story about the damage being caused by too much pressure on the city's underground pipes. Once all the appropriate people are alerted that Audrey is missing, everyone pitches in to solve the mystery. A possible break in the case comes when someone calls in another abduction at the Altair Bay Inn. Nathan and Duke go to investigate and find a slightly loopy Wesley Toomey, who claims his mother, Roslyn, was abducted by aliens. They try to pacify Wesley in order to get more info about Audrey's abduction, but he makes a run for it and, when they give chase, all their electronic and mechanical equipment fails.
Soon, a UFO crashes into the earth behind Wesley's home and he tells Duke and Nathan that he is the only one who can stop the coming alien invasion. Slowly, it dawns on them that Wesley is "troubled" and his fervent belief in the alien stories handed down by his grandfather is what's making them real.
Meanwhile, Audrey is being held prisoner in the same inn where Wesley's mother was taken. Both Roslyn and Audrey are being held in the basement against their will but it seems like Audrey gets the worst of it—her abductor knows more about her than she does. Eventually, Audrey hatches a plan to escape but she can't cut her bonds quickly enough to save Roslyn, who Audrey can hear being dragged away. Later, Audrey makes it to a phone and calls Nathan to tell him where she is.
Everyone rushes to the inn to save Audrey but they are too late to save Roslyn, whose remains they find in a fire. With time running out before the alien mother-ship blows away all of Haven, Nathan, Audrey and Duke all try to stop Wesley's wild imagination from taking things any further.
Audrey tries to reason with him, Duke threatens him and, finally, Nathan convinces him that his grandfather probably went willingly with the aliens to prevent damage to Haven. Encouraged by that possibility, Wesley lets the aliens take him and, as soon as he does, the alien invasion ends.
When Audrey tries to make sense of her kidnapping, she remembers that the kidnapper asked her about the whereabouts of the Colorado Kid, which encourages Audrey to have the Colorado Kid's grave exhumed. Sure enough, the grave is empty—except for a note in Audrey's own handwriting urging her to find the Colorado Kid before "The Hunter" returns. For now, it's a riddle that none of them can make sense of. Unbeknownst to Audrey, however, her abductor is watching her put the pieces of the puzzle together from afar.
Later, while chatting with Nathan, Dwight learns that Nathan got the mysterious tattoo on his arm just so that he would be able to kill Duke if he had to. Dwight understands but warns Nathan to beware of the symbol's dark power.
And William Shatner is along for the ride. Haven returns to Syfy in 2015.
When Audrey and other residents are overcome by a mysterious illness, the truth about the Troubles could be exposed to the outside world.
Take a journey into Haven's past to see the beginning of the Troubles in Part 3 of this digital series.