The sickness outbreak that's been plaguing Haven has reached epic proportions and all hands are on deck to stop it, including Pete, who usually hides the Troubles from the public. Sadly, it turns out that Pete causes this particular Trouble. Even worse, he can't be talked out of it.
After some soul searching, Dwight decides to trust Dr. Charlotte Cross from the CDC with Haven's biggest secret: The Troubles. He starts by showing her his own bullet Trouble and gradually adds more information until she is convinced.
Obviously, Dwight's trust in Dr. Cross is not shared by anyone else in Haven. Everyone else wants to get rid of her, not bring her into the fold. Dwight's decision is making him very unpopular. Nevertheless, once Dr. Cross comes around, she claims she might be able to cure the Troubles if only she had a sample of whatever causes them. Eager to have a cure for the Troubles and more than a little attracted to Dr. Cross, Dwight decides to give her access to the Aether that Mara uses to create and alter Troubles.
Unfortunately, Dwight isn't the only person in town who wants the Aether. Mara convinces Duke that it's up to the two of them to save Haven from the CDC. In turn, Duke releases Mara and takes her with him to Dwight's office where he plans to steal the Aether and let Mara use it to alter Pete's Trouble into something less dangerous.
Duke and Mara don't move fast enough, however, and Dwight gets to the Aether first. Once he hands it over to Dr. Cross, he has every hope that she'll use it to make Haven a safe, normal town. Things get hairy when Audrey herself ends up sick and a member of the Guard's Trouble kicks in at the hospital but, after things settle down, Duke and Mara end up face to face with Pete, the source of the contagion Trouble. Pete begs to be killed by Duke but Duke refuses, until Mara stabs Pete herself. To keep Pete from dying in vain, Duke finishes him off, thereby ridding Haven of Pete's Trouble.
Meanwhile, Vince has been trying to get the Governor to pull the CDC out of Haven only to discover something troubling: The CDC says they don't have anyone in Haven. If that's true, then who is Dr. Charlotte Cross and what is she really going to do with the Aether?