Now that Audrey has somehow been separated from Mara, Duke and Nathan decide to keep Mara on Duke's ship for safe keeping until Dwight gets back in town. They really want to turn Mara over to The Guard but without knowing if Mara and Audrey are physically connected, it's too risky.
Sadly, that's not the only thing Nathan is worried about. He's also worried for Audrey's safety since she's no longer immune to the Troubles. It turns out that it was Mara who was immune and, now that the two of them are separate, the Troubles affect Audrey. This also means Nathan can't feel her any more.
To make matters worse, Audrey and Nathan are called in to solve a new case. A rash of vanishing bodies is sweeping across Haven and Audrey decides to use this opportunity to prove herself to the citizens of Haven, despite all the animosity directed her way.
Audrey and Nathan discover that people have been seeing bright flashes of light and, once the light fades, all that's left is a smoky silhouette of whoever just disappeared. Fearing for Audrey's safety, Nathan asks Audrey to sit this case out and goes sleuthing on his own. In the process, he discovers that The Guard considers him a traitor to his own kind. Later, as he's updating Audrey about the progress he's made, Nathan vanishes too, leaving a dark outline on the floor of the police station.
Nathan isn't dead at all but stuck in a limbo like state. He can see and hear everyone around him, but he can't communicate with them. He can only talk to other "ghosts" who are stuck in the same limbo state that he is.
While Nathan talks to the other ghosts to figure what they have in common, Audrey focuses her attention on solving the Trouble from her side. There is an unexpected twist, however, when Nathan realizes that Mara can see and hear him.
Nathan tries to get Mara to help him but she won't cooperate, not even when The Guard kidnaps Audrey. But when Duke vows to turn Mara over to The Guard and trade her life for Audrey's, Mara has a change of heart. She knows The Guard will torture her if they find out about her existence, so she decides to help Duke communicate with Nathan in order to rescue Audrey.
Once Audrey is saved, Nathan starts to relax until he discovers that one of his new ghost-friends has been killed. There is no trace of the killer except a sign that reads, "even ghosts can die." Looks like someone is stalking Nathan, even in limbo.