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When her hands are somewhat clean, she pulls out her cell phone and texts Mr. Ketch, saying “Lester’s down. Who’s next?” As Mary gets back into her car, Mr. Ketch replies with a list of three names, and locations where the people live. Jody Mills is the third name on the list. Mary starts her car and drives off into the night to continue her murder spree.
At the bunker, Dean turns on the emergency lights as he and Sam try to figure a way out of the bunker. Sam suggests using the garage, but Toni reminds him that the doors are warded and the walls are reinforced steel. Sam also suggests the air duct system, but Toni says the ducts are too small and even she wouldn’t be able to squeeze through.Annoyed, Dean suggests to Sam that they kill Toni to help conserve air for the two of them. But Toni tells Dean that if they get out of the bunker, she is the one who programmed Mary and therefore is the only one who can reverse the brainwashing process. The Boys don’t trust her, but decide to let her live in case she’s telling the truth.
Toni also tells them that the only way out is to pull the manual override, but it’s located outside the bunker. As they’re talking, Sam suggest that since they’re in a bunker surrounded by lore on spells, there must be a spell that will reverse the lockdown.
By lantern light, Dean, Sam, and Toni search through the bunker's library books to find a spell. Sam finds an abrogation ritual that supposedly reverses complex mechanical processes and resets machinery. They learn that they have the ingredients for the ritual, except for one – virgin blood. Since none of them are virgins, they come up with a blood purification spell, deciding that they will use their purified blood for the second spell.
They all cut their hands, bleed into a large bowl, and add the other ingredients while Sam recites an incantation to purify their blood. The mixture flashes red, and they presume the spell has worked. Next, Toni recites the incantation for the second ritual. After she finishes, but bunker begins to shake as if an earthquake is happening, and the emergency lights flicker. The regular lights start flickering as if they’re going to come back on, and the trio starts to think their spell is working. Suddenly, everything stops, the lights go off, and the emergency lights go on again. Toni realizes that Ketch must have realized they’d use magic to escape, so he applied a mystical damper so that no magical solution would work.
In the war room, Dean spreads the bunker’s blueprints on the table. He explains that most of the walls in the bunker are reinforced steel, but there’s one exterior wall that is just concrete. That wall is next to a sewer pipe that goes straight to the surface. Dean thinks that if they can break through that wall, they can climb up the ladder in the sewer pipe and get to the manual override switch.
Later, we see Dean and Sam using pick axes to try to break through the wall. An unknown amount of time passes, and they are both tired. They are also both breathing heavily because the bunker is running out of air. We also see that the wall is damaged, but they are nowhere near breaking through it.
They sit on the floor to rest and try to catch their breath. Sam surmises that it will take them days to break through the wall, and they will run out of air before they do. Both brothers appear winded because their air is already running out.
The brothers begin discussing how they arrived at their current situation. Dean talks about how they recently saved the world and got their mother and Castiel back, and although things weren’t perfect, at least they were together. But now Castiel and Mary are both ”gone”. Sam blames himself for falling for the British Men of Letters’ (BMOLs’) company line and joining their side. He admits that once he was inside the BMOLs, he just followed because it was easier than leading. Dean also discusses how he always expected them to die in a blaze of glory, but as he’s thinking about that, he remembers the grenade launcher and suggests it might help them break through the wall.
Later, Toni tells Dean and Sam that they’re lunatics for thinking about using the weapon – that the explosion could kill them all and cause the building to collapse. Dean and Sam ignore her, perhaps silently accepting that they’d both rather die that way than by slow suffocation. As Sam hauls a reluctant Toni to safety, Dean fires the weapon at the wall.
Sam and Toni are crouching in a hallway when they hear the explosion. Sam immediately returns to the room to find Dean. He calls and searches, but Dean doesn’t respond. Sam walks over to the wall and sees that Dean’s plan has worked – there is a large hole in the wall, and Sam can see the ladder inside the sewer pipe.
Before Sam can do anything, the tunnel caves in and the only exit is obliterated. Sam continues searching for Dean. He ends up in the war room, but by this point he is dangerously weak from inadequate oxygen. Struggling to breathe, he collapses to his hands and knees.
As Sam struggles to breathe, the lights and air suddenly come back on. Sam hears the door open and as he turns around to look, he sees Dean limping through the door. Dean has a large wound on his left leg, but he was apparently able to make it up the ladder and get to the manual override. The brothers are clearly exhausted but happy to see each other alive, as Dean smiles and casually says “Hey, Lunatic.”
Elsewhere (in Sioux Falls, SD), we see Mary’s car pull up to Jody’s house. When Mary knocks, Jody opens the door and sees blood on Mary’s clothes. Mary asks if she can come inside, and Jody lets her in.
Back at the bunker, Dean and Sam are outside and have handcuffed Toni inside the Impala. They are both looking through the trunk for a cell phone, so they can begin warning people. Dean finds a phone and calls Garth to warn him, telling him to take Beth and leave their home. Sam finds another phone and tries to call Jody, but he can’t reach her.
The Winchesters race to Jody’s house. When they arrive, they find Mary (with a bloody nose) tied to a chair, and Jody icing her eye, but alive. Alex is with Jody, and furniture is toppled indicating that a fight has taken place.
Time passes and Jody has been talking to the Boys while Alex has been cleaning the wound on Dean’s leg. Jody tells Dean that Mary attacked her and she thought Mary was a demon. Jody and Alex got the upper hand, and Jody was able to temporarily knock Mary out. Dean feels guilty that Mary tried to kill Jody, but Jody assures Dean it wasn’t his fault.
Dean glares coldly at Mary while Mary taunts Jody for pretending to be a mother to the Boys. Jody tells Dean “that’s not your mom”, but Mary continues taunting Dean, telling him that she’s not all that different from his mother. As this is happening, Sam returns from the car with Toni. The Winchesters tell Toni to reverse Mary’s brainwashing. But she tells them that she was only lying about being able to do that so they wouldn’t kill her. She tells them that the “real” Mary is trapped behind impenetrable psychic walls, and the brainwashing is permanent. Dean prepares to shoot Toni, but Mary’s cell phone rings; it’s Ketch trying to reach her for an update. Dean and Sam ignore the call, but Toni warns them that Ketch and the others will not stop pursuing them, so they should run. Sam and Dean say they won’t run, but they will fight.
A few minutes have passed, and Jody tells the group that they will leave in ten minutes. Dean tells Sam that with his leg injured, he won’t be reliable in a fight, so he isn’t coming with them. Sam protests, but Dean lets him know that he believes Sam can do this without him. When Sam asks what Dean plans to do, he says he is going to save Mary. He believes Mary is still there somewhere and he plans to find her and bring her back. As Dean and Sam say goodbye, Jody says goodbye to Alex, instructing her to meet Sheriff Donna at a safe house.
Once Dean and Toni are alone, Dean tells Toni that she was able to get inside Mary’s head once, so he wonders if she can get him inside Mary’s head to find her. Toni says she may be able to, but she’ll need equipment at the bunker.
Elsewhere, at the BMOLs’ base, Dr. Hess is addressing the remaining BMOL staff. She orders them to kill family members, bystanders, and anyone else who might be a witness to their activities against the American hunters. As this meeting is happening, the scene cuts to an open road and we see the convoy of hunters making their way to the BMOL’s base.
After the staff meeting, Mr. Ketch pulls one of the technicians aside and orders her to secretly locate Mary. The technician conducts a computer search and tells Ketch that Mary is in Lebanon, Kansas.
Dean and Mary:
At the bunker, Dean handcuffs Mary to a chair in the library and asks Toni what equipment she needs to reverse Mary’s brainwashing. Toni tells him the equipment is in the storage area near the dungeon. She prepares to go get it, but Dean stops her, saying he’s unwilling to let her out of his sight. Toni tells him that the BMOLs left her to die, so she has no loyalty to them. She also asks that, when this is over, Dean allows her a head start before coming after her, because she’d like to see her son again. Dean reluctantly takes off her handcuffs.
Sometime later, we see Dean and Mary sitting in chairs across from each other. They both have electrodes connected to their heads.
Toni says that the electrodes will synchronize Dean’s delta brain waves with Mary’s – forming a psychic link. She also says that entering Mary’s psyche will take concentration that she doesn’t think Dean is capable of. She injects Dean and Mary with a drug that’s a combination of a hypnotic agent and a potent sedative. She believes it will help them with the process. Before Toni can inject Dean, he handcuffs her to the table. After she injects him, he falls asleep. So does Mary.
Under the influence of the drugs and electrodes, Dean wakes up downstairs at his childhood home in Lawrence, Kansas. He begins looking for Mary, assuming that her delusion has her located somewhere inside the house. He enters the kitchen, but it’s empty. He starts to go upstairs, but hears a baby. He turns around and sees a crib in the living room; there’s a baby crying in the crib. Dean walks over to the crib and recognizes Sam as an infant. Then he sees Mary, as a young mother, lean over the crib to check on Sam. Mary clearly can’t see Dean standing there. She goes into the kitchen and we see that she’s preparing a peanut butter and jelly sandwich and milk for 4 year-old Dean, who enters the kitchen and sits down.
As Dean looks on, Mary serves the child his food, and tells him there’s pie for dessert. Dean calls to Mary repeatedly and tells her that they need to leave, but she can’t hear him. Dean tries to convince Mary to listen to him, letting her know that he realizes she created this place because it feels safe for her, but he needs her to listen to him snap out of her hallucination. Mary doesn’t see or hear him.
Mary tells young Dean that she only wants good things for him and will never let anything bad happen to him. Dean looks on and says to Mary “I hate you.”
By this point, Mary has stopped puttering around the children and seems to be listening. Back at the bunker, Toni Bevel looks on as a tear streams down Mary’s face while she is unconscious. Back inside Mary’s hallucination, she is also crying as Dean’s words reach her. Dean tells her he hates her, but he loves her because she’s his mother and he can’t help it. He also says he understands her making a deal to save John, because he has also made deals to save someone he loves. He tells Mary that he forgives her for everything. As he’s talking, Mary’s back is still turned to him, but she is crying and can clearly hear him. Dean tells Mary that when this is over, the three of them (Dean, Sam, and Mary) can start over and get things right this time. But to do that, Mary needs to fight, turn around, and see him. After a moment, Mary turns around and looks at Dean. They are both crying and they clearly see each other. Mary says Dean’s name, and he responds.
Suddenly, Dean is awakened. Back at the bunker, we see that Toni Bevel is on the floor – her throat has been cut. And Mr. Ketch is turning off the electrode machine. Dean is still groggy, but wakes up. Mary is still unconscious. Dean and Ketch fight. Despite his injuries, Dean fights bravely and overpowers Ketch. Ketch realizes that he can’t beat Dean in a fight, so he draws his gun and prepares to shoot Dean. Mary (who has woken up during the melee) shoots Ketch through the shoulder from behind. Mary appears fully awake and stares coldly at Ketch with her gun aimed at him.
Dean kicks Ketch’s gun away from him and stands beside Mary. Ketch tells Mary that he knew she and Dean were both killers. Dean tells Ketch he’s right, and Mary shoots Ketch in the head, killing him.
Sam and Jody:
At the BMOL’s base, the operatives (clad in military uniforms and Kevlar vests) gather their weapons and prepare to leave. As this is happening, the hunter convoy arrives and crashes through the main gate, led by Jody Mills. A spectacular military assault follows, during which the American hunters methodically cut down the heavily armed BMOL’s and advance to the central control room of the base. Many BMOLs die, and some of the hunters also die, including Roy.
Dr. Hess locks herself in the control room and calls the BMOL’s hierarchy, demanding that they help her escape. She is told that the resources needed for that are unavailable. She is using her laptop to talk to someone at BMOLs’ headquarters when Sam, Jody, and Roy break into the room.
Dr. Hess reaches for her gun, but Sam has a gun on her and orders her to stop. Hess raises her hands and tries to talk her way out of the situation.
Hess tells Sam that killing her would be a grievous mistake, and she shows him file photographs of Lucifer leaving Crowley’s lair. Hess tells Sam that Crowley is the reason Lucifer is free, and Crowley is now dead. She says the American hunters need the BMOLs to help them defeat Lucifer, who is looking for his son, which means he is tracking Castiel and Kelly. Hess tells Sam that if Lucifer gets his hands on the Nephilim, they will be unstoppable. The voice on Hess’ computer screen (someone who has apparently overheard the entire exchange) tells Sam that he should listen to Dr. Hess. As Walt and Jody look on, Sam briefly considers his options. After a brief pause, Sam says “Pass” and shoots the computer monitor. Enraged, Hess reaches for her gun, and Jody shoots her in the head.
Later, we watch Jody’s truck and the Impala leave the compound, as a series of large explosions destroy the BMOL’s base.
Back at the bunker, Mary starts cleaning up the library. Ketch and Dean were fighting there, and the room is littered with broken furniture and debris. Dean returns to the room with some expired prescription pain killers he found somewhere in the bunker. He notices what Mary is doing and tells her she doesn’t have to do that. Mary tells Dean that everything that happened is because of her. Dean tells her things will be okay, but Mary says it’s not okay. She tells Dean that she realizes she’s been distant and cold since she’s been back, and that by leaving Dean and Sam to work with the BMOLs she was trying to make things right. She says she kept her distance because being with him and Sam -- and seeing what she’d done to them -- was too hard. Dean tells Mary that her deal and everything else that has happened has made him and Sam who they are – and they kick ass and save the world.
Mary smiles in sad acknowledgement, and asks about Sam. She says she’s afraid that Sam won’t be able to forgive her. As they’re talking, Sam enters the room. He walks over to Mary and hugs her, saying she doesn’t need to be scared of him. Dean claps Sam on the shoulder, and tells Sam he’s glad he made it back. Dean hugs Sam, and the family enjoys a reunion.