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The scene opens exactly where “All Along The Watchtower” ended. Dean is outside the house next to Castiel’s dead body, and Sam is upstairs with Jack, the newborn Nephilim who is sitting in a corner of the room.
Dean and Sam are still unconscious, but we see what Dean is dreaming about. He is reliving the night before, when Mary got pulled into the dimensional rip. In Dean’s dream, Mary approaches Lucifer, but instead of getting pulled into the rip, she bursts into flames and Dean looks on in horror as she burns alive on the ceiling again. Dean wakes up abruptly and realizes he was dreaming. He looks over to Sam, who is also starting to regain consciousness. It is the next morning, and we suspect they have been out for hours.
They brothers realize that Jack is gone, and head outside to look for him. Dean asks Sam if Jack can teleport, but Sam says he doesn’t know. The Boys get into the Impala and start looking for Jack.
Meanwhile Jack, who is completely naked and looks like a teenaged boy, is walking along the side of a road, with a look of wonder on his face as he views trees and other creations for the first time.
Next, we see Dean and Sam driving down the road looking for Jack. They briefly discuss what happened the night before, but Dean clearly doesn’t want to talk about it – especially about the fact that Cas is dead. Dean says Jack tried to kill them, but Sam insists that was only because Dean tried to shoot him first. Sam says he was handling the situation and thinks they should have a plan before they go after Jack. Dean insists that they need to get to Jack before he hurts anyone, so they continue driving.
Christine asks Jack where his parents are and Jack says his mother is in heaven, and his father is supposed to be here but isn’t. He says he has to find his father. Christine offers to help Jack do that, but when Jack can’t tell her his father’s address, phone number or email address, she takes Jack’s thumbprint for identification, and leaves the room to search the computer for a match to the thumbprint. When Jack and Clark are alone, they talk briefly, but Jack continues giving strange answers to questions. Clark assumes Jack is high on drugs and asks what he took. Jack says he’s not high, but he is hungry.
Back at the restaurant, Dean and Sam arrive. The other clerk is still inside, and the place is open. Sam goes inside to see if anyone saw Jack, and Dean stays in the car, telling Sam that he’s going to call Jody Mills to ask her to put out an alert for Jack. After Sam leaves, Dean gets out of the car and walks toward the building.
Inside the restaurant, the clerk is arguing with a drunk young woman who wants French fries. Sam asks the clerk if he’s seen anyone fitting Jack’s description and the clerk tells Sam that Jack is at the police station. Posing as a fed, Sam calls the station and learns from the sheriff that Jack is still there. Sam asks the sheriff to hold Jack until he arrives. The sheriff agrees. As she’s on the phone we realize that she hasn’t been able to find a match for Jack’s fingerprints because he doesn’t seem to have any.
Outside, Dean is walking back to the car, and we see that the knuckles on his right hand are bloody. As he approaches the Impala, the drunk woman from inside the restaurant is at the car. She asks Dean what happened to his hand, but he won’t talk to her. She launches into a drunken monologue about her roommate from college, named Becky, who was a terrible person and made her so angry she punched a wall once. Dean won’t engage the woman, so as she’s talking we see her trace something with her finger onto the car window. As this is happening, Sam returns to the car and tells Dean he knows where Jack is. The Winchesters get into the car, and as they pull away we see that the young woman has written the word “b*tch” on the window. She watches them drive away.
At the station, sheriff Christine is at her desk when the lights start flickering on and off. She calls to Clark and Jack, but they don’t answer. Christine hears laughter and voices coming from a break room down the corridor, so she walks towards the sounds. When she arrives, she finds Clark and Jack sitting on the floor in front of a vending machine, eating candy bars. Jack has eaten several candy bars, and apparently likes nougat.
As they’re talking, we hear a high pitched ringing sound (which we recognize as angels talking). Jack groans in pain, grimaces and grabs his head like he is in terrible pain. He tries to leave, but the sheriff tries to stop him. When she touches him, he inadvertently hits her with a shock wave, which flings her into the vending machine. She slumps to the floor, unconscious, as Clark rushes to help her.
Jack, still in pain and with the loud ringing in his ears, staggers into the hallway and makes his way back to the main room of the station. As he’s walking along the corridor, lights explode. We don’t know if Jack is doing that or if it’s the angels, but when Jack enters the main room, he sees Dean. He advances toward Dean aggressively, but before he reaches Dean Sam shoots him in the back with a taser gun. Jack falls to the floor unconscious. As Dean and Sam approach Jack’s body, Christine appears in the doorway with her gun drawn. She demands to know what is going on.
Later, we see that Sam and Jack are locked in a cell, and Dean is being questioned by the sheriff. Dean tells the sheriff the truth – his real name and Sam’s, the fact that they hunt monsters, and that Jack is a Nephilim (and what that is). Having witnessed what she has already seen, Christine seems to believe him.
Back in the cell, Jack wakes up angry. Sam apologizes for hurting him, and asks if he’s alright. That seems to calm Jack down. Jack says that when he gets scared, things happen and he can’t control them. When Sam asks why Jack is scared, he says that the loud, angry voices in his head frighten him. Sam likely understands that Jack is hearing angel radio, but doesn’t try to explain that to Jack. Nevertheless, Jack asks Sam to tell the angry voices that he’s sorry, and Sam agrees to do that. As Sam and Jack talk, we learn that Jack learned how to speak English through Kelly while she was carrying him. Kelly is also the one who told Jack that he wouldn’t be safe when he arrived, so he chose to grow up quickly – which is why he is already a teenager. When Sam asks about Jack’s powers, Jack says he doesn’t understand them. We also learn (from this conversation and the earlier one with sheriff Christine) that Jack remembers killing Dagon, and some other events that happened when Kelly was still pregnant with him. Jack remembers opening the dimensional rip. But when Sam asks him if he can open the rip again, Jack says he doesn’t know.
Jack tells Sam that he has to find his father, who will protect him. When Sam tells Jack that isn’t really what Lucifer does, Jack tells Sam that his mother told him that Castiel – not Lucifer – is his father and will protect him. Sam tells Jack that Castiel is dead.
Meanwhile, Clark has stepped outside the building to smoke a cigarette. Before he can light it, the angels arrive and confront him. We recognize that the drunken woman from the restaurant is an angel. Inside the building, Dean has returned to the cell to talk to Sam. Dean says that he talked to the sheriff and she is letting them go. He suggests that they take Jack someplace private so they can kill him, but Sam tries to convince Dean that Jack is just a kid and they shouldn't kill him because they need him. Before the discussion can get much further, and Dean can open the cage, they hear Clark shout for help from the outer room. Dean rushes to see what has happened.
In the outer room the drunken angel (Miriam) has an angel blade to Clarke’s throat, and is using him as a shield. Dean and Christine look on as Miriam offers to release Clark if the sheriff will kill Dean. Miriam taunts Dean, telling him that he destroys things without caring about who gets hurt, so he needs to die.
Back in the cell, Sam is alone with Jack when the outer door is suddenly ripped off its hinges and two angels (Ish and Lily) enter. Using angel radio, Ish tells Miriam that they have Jack. Instantly, Jack screams and grabs his head, as the angel voices hurt him. Meanwhile, Miriam (who no longer needs to bargain) stabs Clark. Clark falls to the floor and Christine rushes to him and tends to his injury, calling for an ambulance. Miriam and Dean begin fighting. As they are fighting, Dean temporarily gets the upper hand and holds an angel blade to Miriam’s throat. When he demands to know why the angels are here, she tells them that they want Jack and Lucifer. She also tells him that Jack can do almost anything. But she says Jack can’t bring Castiel back, and that Cas’ death is Dean’s fault. Miriam breaks away from Dean and goes back to the cell to get Jack.
Meanwhile, back at the cell, Lily pulls off the door of the cell, and the angels attack Sam and try to take Jack. During the fighting, Sam ends up bleeding on the floor. Thinking he has been neutralized, the angels try to take Jack and leave. But Sam has secretly used his blood to create a banishing sigil. Sam slaps the sigil and blasts the angels away.
Some time later, we see the ambulance taking Clark (who is alive, but injured) away, and the Winchesters are leaning against the Impala talking about their next move. They agree to take Jack back to the bunker. Sam thinks Jack isn’t bad, but Dean disagrees and thinks that even if he seems okay now, he’ll eventually turn bad and they’ll need to kill him. Dean feels that keeping Jack at the bunker endangers him and Sam, but nobody else, so he agrees to the plan.
Later, Dean, Sam and Jack arrive back at the cabin. Dean prepares to build a funeral pyre for Castiel and Kelly. Sam tries to talk him out of burning Cas’ body, but Dean is convinced that Cas can’t be brought back. Sam suggests that they call Chuck to ask him to resurrect Cas. But Dean tells Sam that he already tried that:
FLASHBACK: We have a flashback to the moments when Sam was inside the restaurant and Dean was in the car. Dean leaves the Impala and walks around to the rear of the building where the restrooms are located and prays to Chuck. Dean initially asks Chuck for help. He is clearly angry that Chuck left him and Sam alone, and says that they have lost everything. He demands that Chuck resurrect Castiel, Mary, and Crowley. He pleads, but nothing happens. Furious, he punches the mens’ room door several times, which we realize is why his knuckles were bloody when we saw him return to the car earlier in the episode.
RETURN TO PRESENT TIME: Later that day, Sam takes Jack into the upstairs bedroom where Kelly died and shows Jack Kelly’s body. Jack touches her foot (wrapped in a sheet) but nothing happens. Meanwhile, downstairs, Dean is clearly struggling to control his emotions as he wraps Cas body and prepares to put it on the pyre.
Later, night is falling as Dean douses both bodies with gasoline and prepares to light the pyre. As Sam and Jack look on, Sam asks Jack if he’d like to say anything. When Jack asks what should be said, Sam responds that this is the time when we thank the person, hope that they are going to a better place, tell them we’re sorry, and say goodbye. As they’re talking , Dean says goodbye to Kelly, Castiel, Crowley, and Mary. Sam tells Dean that they don’t know whether Mary is truly dead. But Dean says that Lucifer would have killed Mary as soon as he realized the he’d been trapped. Convinced that everyone they love is gone, Dean lights the fire and the pyre erupts into flames.
In alternate reality universe, we see Mary running. She unfortunately runs right into Lucifer, who slaps her in the face hard enough to knock her down. He pulls her up by her collar and taunts her for trying to run away from him. When Mary asks Lucifer if he plans to kill her, he says maybe not, because he needs her.