A woman in a nursing uniform flees through a house at night as something chases after her. She locks herself in her room as her pursuer briefly pounds on the door and then stops. She barricades the door and sits on the bed, but something grabs her legs and pulls her beneath the bed. As she goes under, she knocks over a nightstand and a picture of John Winchester falls on the floor.
The brothers have pulled over for the night, two hours from nowhere, and the next morning Sam is brushing his teeth when Dean wakes up. A phone in the glove compartment rings and Dean answers it while realizing it's their father's phone. The boy at the other end introduces himself as Adam Milligan and wants to know where John is. Dean explains that John died two years ago, and Adam says that he's John's son.
The brothers drive to a diner to meet with Adam. Sam has checked and determined that Adam has a solid background and his mother is Kate Milligan. There's no father listed on the birth certificate. Dean believes it's a trap and loads up with holy water and silver. As they wait, Sam finds an entry in John's journal noting he was in Minnesota nine months before Adam was born. Adam arrives and the Winchesters explain that their father died in an accident. Adam drinks the holy water that Dean has put in a glass for him and doesn't notice. Adam explains that his mother has disappeared, and John didn't know about him at first. He met Kate, a nurse, when he came into the ER for treatment. As he explains, Dean secretly draws a gun and keeps it under the table. Adam continues, noting that he finally convinced his mother to call John, and he came by several times a year. He uses the silverware without harm and Dean tells him that they're John's sons. Dean doesn't believe it but Adam offers him proof: a photo he had taken with John at a baseball game.
Adam explains that a neighbor saw Kate the night she disappeared, but Adam never found her and the police couldn't find her. As Dean checks the house, Adam asks him about John but Dean insists there's stuff Adam doesn't want to know. Sam has found a news article on grave robberies that took place the year John first visited Windom. The robberies have started up again in the last month and a bartender has also gone missing. Adam doesn't recognize the photo of the bartender. Dean spots scratches beneath Kate's bed and they find an air vent beneath. Dean ends up going down to investigate and finds a section coated in blood and hair.
Adam visits Dean and Sam at their hotel and demands answers. Sam finally ignores Dean and explains that they're hunters. Adam accepts their story because they're his brothers. Adam wonders if Kate's still alive but Dean and Sam aren't hopeful. When he asks to help, Dean tells him no. He figures that John was protecting Adam and they're going to respect John's wishes. Dean storms out and Sam shows Adam how to use a gun despite what he said.
Dean goes to the local cemetery where the funeral director shows him a mausoleum. Dean notices embalming fluid leaking from one of the tombs where a body was stolen. He then goes to a bar where the bartender worked. He meets her wife, Lisa Barton, who knows about cops. Dean spots some photos of the bartender, Joe, when he worked as a cop. He confirms that Joe worked on the grave-robbing case in 1990. Lisa says that Joe had help from someone he called a specialist, but never gave a name. Joe told her that he took care of the grave robber, even through the cops never caught him.
Sam explains to Adam how John died. The power goes out and Sam goes to investigate. They hear something in the vents and Sam gets Adam outside. They run for Adam's truck but something yanks Sam beneath the car. Dean arrives and helps Adam pull Sam clear. Dean fires beneath the truck but the attacker has disappeared into the sewers. There are traces of blood but Sam can't provide a description. They figure the creature is looking for revenge and going after everyone John knew in town. Adam figures it wants revenge.
They go back to Adam's house to get his stuff. Once he's upstairs, Sam insists they should stay. Dean plans to drop Adam off with Bobby and come back to kill the creature. Sam would rather train Adam so he can deal with the creature, and anything else seeking revenge against them. Adam overhears them and insists on undergoing training.
Sam trains Adam in how to shoot and kill monsters. He warns that it's not a job, it's a life, and that all you can count on is family. Dean pulls him to the side and notes that John said the exact same thing, and Sam hated it. Sam admits that John was right, and he finally understands what their father meant. Dean thinks it's too late for them, but Adam has a chance at a normal life. Sam insists the only thing that's real is the monsters that threaten the world. Dean vows to find the creature and goes hunting again. He returns to the mausoleum and finds a secret tunnel leading out. Dean proceeds down the tunnel and finds a large chamber filled with bones and other passages leading beneath the town. He also finds an arm and a pair of glasses belonging to Joe Barton. Hearing a noise, Dean looks back and finds the creature sealing up the tunnel behind him. He checks his phone and discovers it's too far underground to work.
At the house, Sam and Adam seal every possible entrance except one air vent. However, they hear a voice downstairs and go to investigate: Kate Milligan is there. Sam points his gun at her and insists she isn't Adam's mother.
Dean looks for a way out and finds Kate's corpse in a coffin.
Adam yanks the gun away from Sam. Sam tries to convince him to shoot, saying it's not his mother. Adam tells him he knows… and knocks Sam unconscious.
Continuing his search, Dean finds Adam's corpse. Looking around, he spots a stained glass window in the ceiling.
Sam wakes up fastened to a table. He realizes that "Kate" and "Adam" are brother and sister ghouls, not shapeshifters, and they take on the forms and memories of the last bodies they eat. As they start to taste his blood, Kate notes that it tasted different. John killed ghouls' father, and the ghouls think John was the monster.
Dean breaks apart a coffin and uses a strut to break through the window and escape.
As they start to carve Sam up, the ghouls explain that they finally figured out how to get revenge. They killed John's girlfriend and son, but learned John was dead so they went after Sam and Dean. "Adam" boasts that the real Adam was still alive when they ate him. They cut open Sam and drain his blood into dishes, but Dean arrives and shoots "Adam". When Sam warns him they're ghouls, Dean blows off "Kate's" head, the only way to kill a ghoul. "Adam" attacks Dean and they struggle. Dean manages to smash "Adam"'s head in, then release Sam and bind his wounds.
Later, Sam and Dean recover Adam's body and prepare to give it a proper funeral pyre. Sam suggests they contact Castiel and see if they can bring him back, but Dean figures he's in a better place. As they watch Adam's corpse burn, Dean notes that Sam and John are practically the same person, more than Dean ever could be. Sam decides to take it as a compliment.