A group of volunteers organize to search each inch of the forest for missing Flora. While searching, Lee finds Flora's doll ripped apart and bloodied, with a pig's head where the doll's head would be. Shelby, Matt and Lee come upon a decrepit farmhouse and search it for Flora. In the house, they find rotted food and buckets of human waste. They hear pig squealing and leave quickly, heading into the barn. In the barn, they come upon two feral-looking boys suckling from a dead pig.
The boys are removed by the police and will only say one word over and over again: Croatoan. Mason, Flora's dad, arrives to help look for Flora when she has been gone for over 72 hours. They continue to be unable to find her. That night, Mason accuses Lee of having hidden Flora away in order to keep her. After an argument in which Lee is knocked down, Mason storms out.
That night, Matt and Shelby are awoken when Matt gets a call from the cops. He wakes Lee up, telling her that the police found a body and they need to go. Lee panics, thinking it may have been Flora. Instead, it is the burned beyond recognition body of a man -- the cops present Lee with a ring removed from the body. She realizes it's Mason.
Shelby and Matt discover footage of Lee secretly leaving the house that night after Mason and returning four hours later. Shelby insinuates that Lee might have killed Mason and tries to convince Shelby to go to the police. Lee interrupts, angry that Shelby believes that she could have killed Mason.
A stranger named Cricket arrives, claiming he has been called by spirits to the house. Cricket explains that he is a psychic who works with the FBI to recover missing children. The skeptical Millers invite him in, and he walks around the house. He pinpoints the spot where Flora was hiding with Priscilla, finding a bonnet there. He picks it up and tells them that Flora is with Priscilla, a little girl who died in the 1500s. Shelby, who is inclined to believe Cricket's "sight" unlike Matt, gives him permission to perform a ritual to contact Priscilla.
Instead of Priscilla, the ritual conjures up a dark spirit, The Butcher. Cricket calls on a protective spirit. The Butcher reveals that she died centuries before and claims the land, wanting to keep trespassers (like the group of the living) away. She tells Cricket that she does not have Flora -- Priscilla hid her away, off the land, where the Butcher cannot reach. Cricket banishes the Butcher with the word "Croatoan" and then attempts to shake the family down for $25,000 in exchange for the information necessary to find Flora. Lee holds a gun on Cricket to demand answers. Matt gets her to put the gun down and kicks Cricket out of the house.
On his way out of the house, Cricket vows that they will invite him back and whispers something indistinct to Lee that the others can't hear which shakes Lee up. During the documentary interview portion, the producer brings up the whispering, asking if it had to do with Lee's first daughter, Emily. Lee gets upset but confesses the story. The daughter Emily, who Lee had when she was 17, disappeared when she was 4, after Lee left her in a car outside a grocery store while she went in to get sauce. Emily was never seen again.
In the reenactment, Lee visits Cricket to give him the $25,000 in exchange for information. Cricket explains that after he left the house and wandered in the woods, the spirits "downloaded" their information to him. According to Cricket, the Butcher was once Thomasin White, the wife of John White (the governor of Roanoke who went back to England for supplies, leaving Thomasin in charge). Mr. Cage disagreed with Thomasin's decision to keep the colony where they are rather than moving inland, betraying Thomasin. Thomasin's son participates in Cage's plan to put a metal trap around Thomasin's head and leave her outside in the woods to die, after Cage threatens his life.
While Thomasin is in the woods running from wild animals, she is saved by a demon/witch woodland creature, who offers her the heart of the beast she slaughtered to save Thomasin. The creature unlocks the cage around Thomasin's head and implores Thomasin to eat the heart and surrender her soul to the creature. Thomasin does so, returning to the colony and slaughtering the men who overthrew her except for her son Ambrose. The Butcher tells Ambrose that they will move inland as Cage suggested.
In the dramatic reenactment for the documentary, Lee realizes that the colony moved to North Carolina, to the Millers' land, which is why Thomasin claims dominion over that land. That night, Crickets leads Shelby, Matt, and Lee into the woods to confront the Butcher and her group. Cricket offers the Butcher a deal: if she brings them Flora, they will leave. Lee offers to burn the house down to make sure no one ever encroaches on their territory again, angering Shelby who is shocked that Matt went behind her back to agree to burn the house down.
Suddenly, Shelby realizes that Matt has vanished. She goes to look for him and stumbles upon the entrails of an animal. Near the entrails, she finds two of the hillbillies masturbating to the site of a a naked Matt having sex with the demon-witch of the forest. Upset, she goes back to the house on her own.
Cricket assures Lee that the Butcher agreed to the deal. Back at the house, the cops have arrived and Shelby confronts Matt about what she saw and about going behind her back to agree to burn the house down. Matt claims to have no knowledge of the sexual encounter. When Lee arrives back at the house, she is immediately arrested. Matt asks Shelby what she did, but she claims to not know what he's talking about.