After his father's death, Dean goes to see Missouri Mosely at her cabin in the woods, leaving Sam behind. He tells Missouri that John told him that there would come a time when he would have to kill Sam, and insists that he can't handle the thought of ending his brother's life. He breaks into tears and Missouri holds him and tells him to rest for a bit.
Later, Dean goes out on the porch and Missouri brings him a cardboard box that John left to him. Inside are old family photos and letters, including a photo of Sam and a young woman.
Fifteen Years Ago
John calls young Dean down to dinner, where Sam's school teacher Susan Lyle is cooking. Sam tells her that Dean has been acting strange recently, and John admits that Dean is at an awkward age. He invites Susan to join them for dinner and she agrees. Sam is talking to Susan and then hesitates, and John tells him to speak up. The young boy finally says that he wonders if what they're doing now is what it would be like if Mary was still alive. Embarrassed, John tells Susan to ignore Sam's comment but the teacher assures him that it's fine.
That night, John wakes Dean up and takes him out to practice hunting, leaving Sam sleeping peacefully… or so they assume. Father and son track down the Beast of Bray Road, a giant moose-like monster, and Dean complains that they don't need Susan. John insists that Sam needs a mother figure but Dean tells his father that the two of them should be enough for Sam. They spot the Beast and John fires, wounding it, and sends Dean after the creature to cut it off before it gets to the river.
As Dean runs through the woods, he trips and falls down the slope. The Beast doubles back and prepares to kill him, but then explodes in a huge burst of blood and guts. Sam steps out of the woods, covered in the creature's gore, and says that he doesn't know what happened or why he is there. As John comes running up, Sam passes out.
John takes the boys home and calls Susan for help. She willingly comes over and John claims that the boys were dragged into training for the job he does. However, he refuses to elaborate further. Susan is eager to help and explains that she had a son and a husband a long time ago, and they died in a car accident. John assures her that she can stay with Sam and Dean as long as she wants.
Later, Susan is working in the kitchen when Sam comes in. He gives her a star necklace that he made himself. Susan bursts into tears and hugs him in gratitude. John is in the living room and hears someone outside. He runs into the kitchen and shoves Susan and Sam to the ground as the man outside opens fire. Dean comes running from downstairs and John tells him to protect Sam while he goes after the shooter. Once he leaves, Sam tells Susan that they will have to move now that the bad guys know where they live again. Susan says that Sam can come with her again and touches the boy's head, knocking him out as Dean demands to know what she did.
John gets into the Impala and drives off the shooter, pushing him into a guardrail on a bridge. The shooter, Anderson, gets out and explains that he's a hunter, and that he was trying to kill Sam. Anderson knows that Sam isn't a normal human being. John vows to kill Anderson rather than let him hurt Sam, and Anderson tells him that he's making a mistake by leaving Sam with Susan.
Susan drives away in her car with Sam still sleeping next to her, her eyes solid black. She's unaware that Dean is riding his skateboard and hanging onto her rear bumper.
Anderson tells John that Susan offered the yellow-eyed demon her assistance in return for his bringing back her son and husband. The hunter knows that the demon plans to one day have Sam lead an army against humanity, wiping them out. John insists that it isn't true and prepares to kill Anderson. The hunter grabs the gun and tries to shoot, but John stabs him in the chest and then shoves him off the bridge.
Susan goes to a junkyard, knocking Dean off of her car. She says that she's taking Sam somewhere special, but Dean refuses to let her pass, telling her that a demon wouldn't understand that families are special and there can be no substitutions. Before Dean can attack, Susan unleashes the yellow-eyed demon, which forms a giant robot body out of the junked cars. As it moves toward Dean, Susan takes Sam away but he wakes up and she tells him that he's going somewhere safe. Dean gets past the robot demon and tells Sam to run. Sam leaps out of Susan's arms and runs to his brother, and Susan grabs a steel rebar and says that it's Sam's last chance. She promises that she'll be his mother forever, and Sam admits that he always wanted a mother... but for him and Dean.
The yellow-eyed demon tells Susan to kill Dean so they can deal with Sam. Susan runs at the brothers, swinging the rebar... and then hits the robot directly in its glowing yellow eye. As it screams in fury, John drives into the junkyard trailing a chain. He draws a gigantic pentagram in the dirt using the chain and then casts an exorcism ritual, banishing the yellow-eyed demon from its current body and out into the night. The robot body falls apart into its component parts, burying Sam and Dean.
A desperate John scales the mound, looking for his sons and remembering how Anderson said that Sam would destroy humanity. As he kneels in despair, Sam and Dean call to him and climb out of the wreckage. Sam tells Dean that even though he knew their mother Mary longer, he thinks that now they're equal in their grief. The sun comes up and the Winchesters turn to admire the sun.
Sam finds Dean at Missouri's cabin and hesitantly climbs up onto the roof where his brother is sitting. They turn to watch the sunrise, and Dean reminds his brother of how John always liked to watch the sunrise after a night of hunting monsters.
Later, the brothers are on the road again. As Sam sleeps, Dean promises to himself that he'll sacrifice anything to make sure that Sam lives.