Meg picks up John’s cell phone and tells Dean that they’ll never see their father again. Dean angrily hangs up the phone and Sam asks him what Meg said. Dean grabs the Colt and heads out of the motel room, telling Sam that the demon is probably coming after them. Sam tells him that they still have three bullets left, but Dean tells Sam that they don’t know what else is out there.
In the Impala, Sam and Dean discuss what to do. Dean figures that Meg is probably keeping their father alive so they can trade him for the gun. However, Sam thinks that Meg has probably killed their father since she didn’t mention any trade on the phone. Dean yells at Sam for thinking like that, and Sam says he just wants to "do the job and insists that their father would want them to keep going. Dean refuses to believe that his father is dead and insists that they head to Lincoln to figure out which demons took John. Sam scoffs at the idea that Meg left a trail. Dean sees that Sam is probably right and says that they’re going to need help.
Early that morning, the Impala pulls up to a salvage yard. Inside, Bobby Singer brings two flasks over to Dean. Dean asks if they have holy water in them, and Bobby tells him that one has holy water and the other holds whiskey. They sit and talk, Dean remembering how the last time they saw Bobby he threatened to blast John full of buckshot. Behind them, Sam is reading an old book. Bobby walks over to him and Sam, pointing to a circular diagram, asks Bobby if the protective circles really work. Bobby confirms that they do, and tells him how if you get a demon inside, they’re stuck. Bobby tells the brothers that they must be in some serious crap, mainly because he usually only hears of three demonic possessions a year, but this year alone he’s heard of twenty-seven. Bobby figures that there must be some kind of storm coming, and the Winchesters are smack in the middle of it.
Bobby's dog starts barking outside. Bobby heads over to the window and sees the dog’s chain is hanging without the dog attached. Meg bursts through the door and tells them to cut the crap. Dean hurries over to her with the flask of holy water, but Meg waves her arm and Dean is flung against a wall. Meg demands the Colt. Sam lies that they buried it, but Meg doesn’t believe him. She asks if they thought she wouldn’t find them, and Dean, waking up, tells her that they were counting on her finding them. He glances at the ceiling, and Meg follows his eyes to see that she's trapped beneath a Devil's Trap.
Meg sits tied to a chair inside the protective circle. Bobby informs them that he’s salted the doors and windows to keep all other demons out. Dean begins to question Meg about their father’s whereabouts, and they get into a yelling match. Meg claims that John died screaming, and Dean slaps her. Bobby warns the boys that Meg is just a harmless girl that has been possessed, and they can't hurt her. Upon hearing this, they boys realize that they can perform an exorcism to save Meg. Sam begins to speak in Latin and Meg begins to groan. Dean tells Meg that she’s going to burn in Hell unless she tells them where John is, and Sam continues speaking Latin phrases. As Sam speaks, a wind picks up inside of the house. Meg still insists that she killed John, and Dean screams at Meg that their father cannot be dead. Sam continues reading and Meg starts to mutter that John will be dead, and Dean tells Sam to stop reading long enough for Meg to admit that John really isn’t dead. She tells them that John is inside a building in Jefferson City, but doesn’t know who is holding him. Dean then instructs Sam to finish with the exorcism; Meg tells Dean that he promised they’d stop if she told them where John was, but Dean informs her that he lied.
Sam keeps on with the exorcism, but Bobby tells the Winchesters that the exorcism might kill her due to the seven-story fall she took. Only the demon is keeping her alive. Dean argues that she needs to be put out of her misery. Sam hesitates but finally continues. Meg’s head jumps forward and backward as her eyes turn black. Sam finishes and a blast of black smoke comes out of Meg’s mouth. She wheezes and blood begins to drip from her mouth. Dean tells Bobby to call 911 and they lift her out of the chair. Meg thanks them and whispers that she's been trapped for a year, forced to witness everything the demon did. She tells Dean that John is still alive and how the demons want them to come for John, and that the demons are keeping John by the river. Meg gasps for breath and utters the word “sunrise,” and then dies.
Outside, Bobby tells Sam and Dean to leave and he’ll handle the paramedics when they come for Meg’s body. Bobby hands Sam a book and wishes them well. The brothers drive off in the Impala.
Later, the brothers park at a rail yard and look around. Dean loads their weapons and Sam looks through the book that Bobby gave him. He grabs a white grease pencil and draws a symbol on the trunk of the car. Dean freaks out when he sees it, but Sam explains that the symbol will stop demons from getting into the trunk, and they’ll leave the gun in the trunk where it’s safe. The brothers argue about whether or not they should use the gun and whether or not their father would be angry if they wasted the remaining three bullets in order to save him. Sam complains that Dean is the one who dragged him into the whole thing, and he's going to finish it once and for all. Dean accuses Sam of being selfish, but Sam argues that the gun is their only leverage against the demons. Finally, Dean reluctantly agrees to keep the gun in the trunk.
In Jefferson City, the brothers walk along the shore and Dean tells Sam that he knows what Meg meant by "sunrise." he points out an apartment complex named Sunrise Apartment Building. Dean figures that the people in the building are being used as human shields and the demon is probably hiding among them. Dean concocts a plan to pull the fire alarms to get all the humans out, and Sam reminds them that the city will respond in exactly seven minutes.
Sam slips into the apartment building and pulls the alarm. Inside, a demon-possessed couple checks on John, who is unconscious and tied to a bed. Outside, Dean goes up to a fireman and asks if the building is on fire, then feeds the man a story about having a Yorkie upstairs. The fireman ushers Dean aside, while Sam sneaks over and breaks into the fire truck.
In the apartment building, Sam and Dean walk down the hallway in stolen firemen suits. Dean, using his EMF detector, searches for the demons, and gets a reading on the detector outside one of the rooms. Inside the room, the demon-possessed couple hears knocking on the door. Through the peephole she sees Sam and Dean, unrecognizable in their firemen suits, and they tell them they have to evacuate. The woman unlatches the door and Dean kicks in the door, knocking her back. Sam and Dean spray the demons with holy water from their packs and the demons scream. They lock the demons in a room and Dean salts the doorway, assuring that they won’t get out. The boys take off their firemen suits and rush over to their father, confirming that he’s still alive. Dean starts to cut the ropes holding John down, but Sam stops him, thinking that he might be possessed. Sam takes out his holy water and drops a little on John’s face. John comes to and wonders why Sam is splashing water on him. He tells them that the demons have been drugging him and then asks the boys about the Colt. They assure him that it's safe and Dean cuts his father loose.
Outside, a group of residents wait to get back into the building. One man gasps and then his eyes turn black. He walks towards a fireman, and the fireman is possessed as well. Upstairs, Sam and Dean help John out of the room as the two demon-possessed humans hack through the door. Sam pours salt across the door and then they go down the fire escape. Suddenly, Meg's assistant demon tackles Sam, and Dean comes to his brother's aid. The demon telekinetically throws Dean through the air and into a windshield of a car, then starts beating Sam until Dean shoots him with the Colt... that he had supposedly locked in the Impala. Dean picks up Sam and rushes over to help John as well, and gets them both into the Impala.
Sam and Dean take their father to a cabin, and Sam pours salt along the door and window frames. He worries that they were followed by one of the demons, but Dean assures them that they won’t be able to get them here. Sam thanks Dean for saving his life, and has to admit it was a good idea that Dean kept the Colt. They worry that they're killing innocent humans to stop the demons, and Dean admits that he didn't hesitate to kill innocents to save John and Sam. John comes over and tells Dean that he did the right thing, using the Colt. Dean wonders why John isn't mad that he used a bullet, and John says that Dean is always the one who has watched out for them when they became obsessed.
The lights flicker and a wind starts up. John rushes over to the window and tells the boys that the demon has found them. Dean tells his father about how Sam tried to shoot the demon, but it vanished when he did so. John assures his sons that he won’t miss, and demands that Dean give him the Colt. Dean realizes that John would be furious when learning he'd wasted a bullet, and points the Colt at his "father." When Sam comes back and asks what’s going on. Dean tells him that John isn’t their father, it’s a demon. John asks Sam to trust him, and accuses Dean of losing his mind. Sam hesitates, and then sides with Dean. John dares Dean to shoot if he's so sure, but Dean can't bring himself to do it. "John" then reveals yellow eyes and telekinetically slams them into the walls, knocking the gun out of Dean's hand.
The Yellow-Eyed Demon picks up the gun and Sam growls that he’s going to kill the demon. Unimpressed, the Yellow-Eyed Demon explains that he's too powerful for holy water to affect, and tells Sam to pick up the gun telekinetically, but Sam can't. It tells the boys that their father is trapped inside of him, so when he kills them, he'll have to helplessly watch the Yellow-Eyed Demon kill his sons. Then the demon says that the brothers killed the demons in Meg and her assistant, and they were his children. Sam asks the demon why it killed Mary and Jessica, and the Yellow-Eyed Demon tells Dean that Sam was about to propose to Jessica before she died, and that got in the way of its plans for Sam and all the children like him. Dean tells Demon John to get it over with and get things over with. The demon tells Dean that he needs his family more than his family needs him, and Sam is clearly John’s favorite son. Dean snaps back that the Yellow-Eyed Demon is probably really proud of his family too, except that Dean killed them. The demon makes Dean bleed from the inside out. Sam calls out to his brother, and struggles to get loose to help him, without success. Dean tries to reach John, pleading with him to stop the Yellow-Eyed Demon, but the blood continues to pour out of his body. Sam stares over at the gun as Dean continues to plead. The demon’s eyes transform back to normal eyes just as Dean slumps over. John starts crying to himself to stop, and Sam falls down from the wall. He grabs the Colt and points it at John, who switches back to the Yellow-Eyed Demon. The demon tells Sam that if he shoots him, he’ll kill his father too. Sam says that he knows and shoots the demon in the leg. Dean falls from the wall, and Sam goes to his side. John tells Sam that the demon is still inside his body and yells at him to shoot him in the heart using the last bullet and end it now. Sam cocks the gun, but Dean yells not to do it. Sam lowers the gun, hesitates, and before he can shoot, a burst of black smoke pours out of John’s mouth and disappears through the floor.
Sam drives the Impala down the road with John in the front seat and Dean lying in the back. Sam tells them that they’re ten minutes from the hospital. John scolds Sam for not killing him and says he thought they were in agreement. Sam tells him that killing the Yellow-Eyed Demon doesn’t come before everything. He reminds his dad that they still have the Colt and one bullet, and they can start over. Suddenly, a semi-truck slams into the Impala. Glass shatters and metal tears and the car and semi slide across the road. The demon-possessed truck driver looks through the windshield at the Winchesters, apparently dead.