|At a suburban home, a terrorized mother grabs her baby and runs upstairs, leaving a trail of blood. She tries to call out but discovers that the phone line has been cut. The woman hides under the bed as her pursuer comes up the stairs and walks to the bedroom door, and then keeps going. The woman sees a dead man lying nearby and manages to muffle her cry, but something grabs her and pulls her out from under the bed.
Dean, Lisa, and Ben pack into their new neighborhood and Dean checks the demon-hunting gear in the Impala. He goes inside to help Lisa and Ben pack, and Lisa tries to reassure Ben that their moving is for the best. Ben starts to go outside, but Dean asks him to stay
Sam is posing as an agent and investigating the missing baby and the death of its parents.
Lisa and Ben are upset to discover that Dean has ordered in pizza so that they don't have to go out.
Sam calls Samuel, who is tracking the disappearance of babies from locked houses. Sam isn't sure that it is a supernatural incident, and Samuel wonders if he's focusing on their struggle. Sam notices that the security system belongs to the Harper Caine Company, and asks Samuel to see if the other homes were protected the same way.
Dean goes out to the garage and discovers that Ben has opened the Impala and is looking at a gun. Ben wants Dean to teach him how to shoot, but Dean angrily tells him to forget it.
Samuel calls Sam and tells him that his suspicions were correct, and there's another family using the alarm system that fits the profile.
Lisa comes to see Dean and ask why he yelled at Ben. She wonders if they're safe and Dean admits that he doesn't know. Lisa insists that they'll have to move on with their normal lives eventually, but Dean is scaring her now.
That night, Sam goes to the house of the next victims. He finds the couple dead, covered in blood, and footsteps leading away. Sam follows them to a closet, and a security guard emerges and attacks him. Sam stabs him with a silver knife, and the wound hisses smoke. The creature flees and Sam starts to follow, but then hears a baby crying. He investigates it and finds it hidden underneath the table.
Dean is preparing his home against supernatural entry when Sam calls and says that he needs his help. Dean doesn't want to have him in his life, but when he learns what Sam has, he goes to meet him.
Dean makes sure that Lisa knows how to handle a gun. He's reluctant to go, but Lisa insists that he go and deal with the situation. Dean drives to meet Sam, but they realize they have to get some baby supplies, first. They go to a shopping mart and Dean admits he knows about babies by helping with Lisa's niece. As the check out, the baby starts crying and the brothers have no idea how to make it stop. They realize it needs a diaper change but have no idea what to do. An elderly woman finally comes over and helps them. However, Dean glances at the security cameras and sees the woman's true image as a shapeshifter. She runs for it but Sam manages to grab the baby while Dean tackles the shapeshifter. He tries to stab it, but a security guard grabs Dean and pulls him off. He's forced to run after Sam and they drive away, unaware that the shapeshifter has memorized their license plate.
As they drive, the brothers wonder how the shapeshifter found them. Sam figures that it's been following him since he left the house. Meanwhile, the shapeshifter kills a state patrolman and puts out an alert on the license plates.
The Winchesters hole up at a motel and Dean starts bonding with the baby. Sam comments on it and Dean admits that he's had a lot of practice dealing with Ben, and is starting to consider him his son. Dean says that given how they grew up, he wants to give Ben a different life. Sam suggests that Dean might be overly protective, just like John treated them. Dean figures that it's only temporary, but Sam warns that John said the same thing and wonders how Dean can avoid turning into John. Sam then realizes that the father of one of the victims wasn't in the house and is still alive. Dean tells Sam to go without him while he stays and watches the baby.
Posing as an FBI agent, Sam goes to see the father, a mechanic named Jimmy. He confirms that the mother cheated on him and he realized she was lying and avoiding sex. Then she became pregnant and insisted he was the father, but Jimmy knew otherwise.
At the motel, Dean is trying to sleep when suddenly blood sprays out of the crib. Dean hears the baby crying and discovers that it has shed its skin and taken on the appearance of a baby on the diaper pack.
As Dean tends to the baby, the manager knocks on the door and says there have been noise complaints. When Dean refuses to let him in, the person outside breaks in. Dean attacks him and discovers it's the shapeshifter, posing as a state patrolman. It says that the baby should be with their father, and attacks Dean. He manages to hold it off long enough for Sam to arrive and shoot it.
As they drive away, the brothers figure that the shapeshifters reproduce by infiltrating human society and breeding with human women by posing as their husbands when the men are away. Sam suggests that they take the baby to Samuel. Dean is skeptical but admits that he doesn't have any better ideas. They take the baby to Samuel's compound. Dean is reluctant to hand him over and admits he doesn't trust Samuel or the Campbell hunters. Sam finally takes the baby and gives it to Samuel, who talks about when Mary was a baby. Samuel then says that they'll raise the baby, but Dean wonders if they're going to study it. Christian wonders if Dean is obsessed with torture from his time in the pit, and Mark figures that it could become an expert hunter. Dean insists that he doesn't trust them since they don't know how Samuel and Sam came back. Dean backs off and Samuel gives the baby to Christian to raise with his wife, Arline. Dean figures that Christian isn't qualified to be a parent because he's a hunter.
Before they can resolve the issue, they hear dogs barking outside. Samuel has Dean and Sam take the baby to the panic room while the rest arm up. A shapeshifter wearing Samuel's form bursts in and demands its child. Gwen shoots it without affect and Mark attacks it, but it breaks his neck. Samuel and Christian shoot it with tranquilizer darts and it loses its grip on Gwen before it can kill her as well. As Christian goes to get silver nets, the shapeshifter ejects the darts from its body and advances on Samuel.
In the panic room, Dean and Sam hear the fight outside and Sam finally goes to investigate. However, the shapeshifter breaks down the door, wearing Sam's form. It knocks Sam aside and then takes on Sam's form. Dean refuses to hand it over and the shapeshifter grabs him and starts choking him. It takes the baby... and then chokes Dean unconscious.
Later, the hunters survey the wreckage and Dean demands to know what the shapeshifter is. Samuel explains that it was the Alpha Shapeshifter, the first one that spawned all of the rest. They don't know why it has babies, and Dean wonders how they can kill it. Samuel admits that he's not sure if they can.
As Samuel and Dean go, Dean realizes that the shapeshifter at the hotel mentioned having a father. Dean wonders why Sam didn't say anything when he heard it, and realizes that he and the others wanted to use the baby as bait to lure in the Alpha. Sam denies it and Dean seems to accept his explanation.
Back at the safe house, Samuel calls someone about how he failed to capture the Alpha, but promises that they'll find it and bring it in.
Dean returns home and discovers that Ben is out on a bike ride. He looks nervously out the window, and then admits he doesn't know whether to watch over his newfound family, or get as far away as possible. Dean admits he doesn't want to act like his father. Lisa says that she doesn't know, but she does know that Dean is a hunter, and things are different now that he knows Sam is out there. Dean insists that he wants to be there for her, but she says that being a hunter isn't a bad thing. However, she tells him that they can't have this discussion every time, and tells him that he has to go. However, she tells him to come when he can, and come back in one piece. Dean wonders if they can pull it off, and Lisa insists that it's worth a shot.
Dean goes out, uncovers the Impala, and hits the road, smiling.