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Now that Duke and Mara (but mostly Mara) have killed Pete, the contagion Trouble that Dr. Cross found so fascinating has vanished. Nevertheless, she sticks around and keeps working on an overall cure for the Troubles.
It isn't long before there is another Trouble to study. When Marcy, a worker at a local café, falls to pieces and a teenage boy transforms from muscular to skinny in a matter of moments, Nathan and Audrey discover that this new Trouble can alter people physically. Soon, they track the Trouble down to Samantha, the daughter of the café owner. Even though Samantha's Trouble is somehow having a positive affect on Audrey's sickness, Audrey decides to help talk Samantha down anyway. When Audrey gets to the café she sees that Samantha's Trouble has turned Samantha's mother Janet into a little girl.
Once Audrey helps undo the Trouble, Samantha's mom reverts to normal and Audrey's cells start deteriorating again—something that has been happening very slowly since she and Mara split into two different people.
Dr. Cross promises to help Audrey and, when questioned about why she hasn't reported in to the CDC, she says that she's scared the CDC will bungle the situation. That explanation is enough to satisfy Audrey and Dwight but not Vince, who thinks that Dr. Cross has her own agenda.
Since everyone in town has been trying to get their hands on the rest of the Aether, it isn't much of a surprise when it goes missing. Lots of blame gets spread around before Nathan and Dwight discover that a member of The Guard stole the Aether. The question is why?
Duke wanted to get his hands on the Aether so he could convince Mara to help him alter one of his Troubles. Not that he would have to do much convincing. Mara seems to have fallen for Duke and refuses to leave his side, even when he releases a Trouble that could kill them both.
Now that Dr. Cross is definitely sticking around in Haven, Dwight intends to pursue her romantically but he has no idea that she is secretly studying Audrey. Is it to help her, or hurt her?