A man at home sits down at his computer. He hears someone come in and assumes that it's his wife Barb. He calls and gets no answer, and then goes to close the window against the rain. He sits back down and goes to work, and then something picks him up, slams him into the wall, cuts off his hand and feet, and then carves a sigil into his chest.
Sam is driving through the night and Dean wakes up and takes a drink from Bobby's old flask. He insists that he's honoring Bobby's memory, and figures that it's better than Sam pursuing their current case. Four men had their hands and feet cut off and were thrown hard with superhuman strength. They go to the morgue to check on the most recent victim. The coroner, Eddie, tells them that the most recent victim managed to bite his attacker. However, the DNA is of nothing human. As they leave, Sam tries to analyze the symbol. He suggests they get something to eat, but Dean says that he should go ahead while he mingles. Sam realizes that he wants to go to a bar and Dean immediately takes off.
Dean gets to the Cobalt Bar and chats with a woman, Lydia. She immediately picks up on Dean's innuendo, and they talk about Dean's fake job as an investment banker. However, they soon end up at her apartment.
A man, Jerry, is at home and goes to the door when someone knocks. His visitor throws him across the room, cuts off his hands and feet, and then carves the same sigil into his chest.
The next morning, Dean meets back up with Sam as they check out the new murder. Sam admits that he couldn't identify the symbol and that they'll need an expert. Inside, they talk to the chief detective, Charlene Penn, who tells them what happened. Sam notices a teenager outside and goes to talk to him. He says that he lives nearby and was friends with Jerry. He insists that Jerry's wife Ann wasn't happy with him because he had a one-night fling. Afterward, Sam tells Dean what he found out but admits that the wife couldn't have been responsible. Dean realizes that he left the flask at Lydia and calls her, much to Sam's surprise. Lydia abruptly dismisses him and says that she has to go, and then hangs up. Sam hears the whole thing and thinks it's amusing. Meanwhile, at home Lydia contemplates her pregnancy.
Later, several woman gather to help Lydia deliver her baby. Once she gives birth, they name her Emma and move onto the next woman.
At the local university, Dean and Sam talk to Professor Morrison and ask him to identify the symbol. He asks for payment, but the brothers have nothing to offer him except the thanks of a grateful nation. Morrison asks them to get a green card for his housekeeper. Once they leave, Dean complains about how Morrison is the best they can do now that Bobby is dead. Lydia hasn't called him back and he leaves to get the flask.
Lydia is surprised to see Dean and doesn't even remember his name. She tells him that she's been busy and says she has the flask. As she goes to get it, Dean comes in and is surprised to discover that she has a 2-year-old girl. Lydia admits that it's his and Dean goes over to admire her. Sam calls to get him come back so they can go to the crime lab. Dean overhears the baby, Emma, actually talking. He tells Sam that he'll call back and hangs up.
Sam goes to the morgue on his own to check on the most recent victim. Penn is there and tells Sam to wrap it up because they have other cases. Eddie mentions that the FBI is involved because the serial killings cross state borders. Sam asks for the files, and notices that the victim has a matchbook from the Cobalt Bar, the same bar that Dean met Lydia. It turns out that all of the victims went to bars and had flings just before they got killed.
The older woman, Madeleine, arrives at Lydia's house with an associate. She goes inside, unaware that Dean is watching the house. As she goes in, Sam calls Dean. Dean tells him that something isn't right but that he doesn't need backup yet. Sam tells him what he's found out, including the fact that the local victims went to the Cobalt Room. Dean hangs up when Lydia comes out, and he watches as a now five-year-old Emma leaves with Madeleine. Lydia tells her daughter to make them all proud and then watches as Madeleine drives away with the girl.
Dean follows them to a seedy part of town and watches as they go into a warehouse. He goes back and tells Sam what he's discovered, explaining that Lydia didn't have a child when he was there the first time. Sam thinks that he's obsessed and doesn't take him seriously. As they talk, Morrison calls with information.
At the warehouse, Madeleine begins a ritual with Emma and other girls. She says that they perform the ritual in honor of the tribe and kill in honor of the one who created them, and tell each of the girls to eat a piece of meat. Emma hesitates and Madeleine tells her to eat, and the girl does so.
Sam and Dean meet with Morrison, who goes on about all the work he did. He finally tells them that the symbol belongs to the Greek goddess of Harmonia, who created the Amazons. The symbol is an occult talisman to the Amazons, who had no use for men. The Amazons cut off the hands and feet of the males who impregnated them.
Charlene calls her fellow Amazon Madeleine and warns her that Dean and Sam aren't who they claim. She's identified them as hunters, and Madeleine says that they'll dispose of both of them.
Dean goes through Bobby's books trying to find something on Harmonia. Sam checks the Internet and confirms that the Amazon population was decimated and made a bargain with Harmonia. Harmonia turned them into monsters, but there's no indication if it takes something special to kill them. The lore says that they gave birth within 36 hours, and the babies grew to adulthood in a few hours. The mating cycle is every two years, and the murders always happen in different towns every two years. Dean and Sam realize that Emma is Dean's kid, even though he used protection.
Madeleine tells the girls, now teenagers, that they are close to fulfilling their tribal destiny. She brands each one on the wrist and says that now they will learn how to endure and inflict pain.
The brothers go over Bobby's files and Sam notes that the Amazons would have wanted to breed with rich, successful guys. Dean admits that he was posing as investment banker at the time. One paper moves on its own and Sam confirms that there are electromagnetic readings all over the place. However, he points out that there are power lines nearby, making the device useless. Dean isn't convinced and suggests that it might be Bobby. Sam refuses to accept it, figuring that they're only considering the idea because they want Bobby to be alive. Undeterred, Dean says that the paper, which is written in Greek, could be useful. Sam takes it to Morrison and tells Dean to stay in the room and lock the door.
At the university, Sam asks Morrison to translate the paper. He offers to remove his (non-existent) wiretap in return for his help.
Dean is checking the Internet when there's a knock at the door. He draws a gun and goes to answer it, and discovers that it's Emma. She explains that she's trouble and Dean is the only one who can help her because he's her father. Emma explains that the Amazons have been watching him, and that she escaped when the women who watched over them changed shifts. When Dean wonders why Emma is there, she tells him that they're expected to do terrible things without questioning. She shows Dean the brand and insists that she doesn't want to be like the Amazons. Dean lets her in and Emma asks him to get her away from the Amazons. When Dean hesitates, Emma says that she hopes he'll protect her long enough so she can get away and then she'll leave him alone. She figures that Dean doesn't want her and Dean admits that it isn't a normal situation. However, Emma says that it's her last chance to have something normal.
Morrison admires the paper until Sam gets him back on track. He tells Sam that according to the ritual, the child must kill her own father.
Emma says that she's hungry and asks if Dean will help her. He wonders if she really wants help.
Charlene finds Sam at the university and he realizes that she has the Amazon brand. She throws him down the hall and draws a knife, but Sam manages to shoot and kill her. However, he realizes that his phone was smashed in the fight.
Emma says that the other Amazons will hunt her down and she has to get out now. However, as soon as Dean's back is turned, she draws her knife. However, Dean spins around, gun aimed, and says that he knew she'd try to catch him off guard. Emma insists that she has to kill him, and points out that Dean would have killed her 30 second ago if he could bring himself to do it.
Sam drives back and hears Emma talking. She says that either she or Dean has to kill the other. Dean points out that she hasn't killed anyone yet and she can walk away, but Emma says that she has no choice. Sam smashes in and Emma begs Dean to help her. As Dean stares at her, Sam shoots her dead. The brothers go to the warehouse only to discover that the Amazons have abandoned the place and moved on.
As the brothers drive off, Dean tries to reassure Sam, saying they'll be ready when the Amazons resurface. An angry Sam finally accuses Dean of letting Emma walk, when he wouldn't let Sam's friend Amy live. Dean denies it but Sam says that his heart isn't in it. However, his brother says that Sam isn't handling it either. Sam tells Dean that he doesn't care how he handles it as long as he doesn't get himself killed. Dean tells him that he'll do what he can and tells Sam to shut up about it.