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The Winchesters are with Bobby in the hospital when Castiel drops by. Castiel says he is now a fugitive, isolated from heaven and unable to heal Bobby’s paralysis. To stop Lucifer and the apocalypse, he wants to find God who he thinks is on earth and he needs Dean’s bull amulet, which glows in God’s presence, to do it. At first, Dean refuses to give it to him, but then hands it over when Castiel changes his request to an order. Then Bobby’s phone rings and it is Rufus calling for help.

The Winchesters drive to an isolated town in Colorado to rescue Rufus but instead, find Ellen Harvelle and a small group of survivors hiding in the local church. They tell of a town overrun by demons with everyone who isn’t dead being demon possessed. Ellen says that she got separated from Rufus and her daughter, Jo, soon after they got into the town.

While Dean prepares the survivors for fighting demons, Sam and Ellen go out to find the missing hunters. But Sam is captured by a demon-eyed Rufus and Ellen barely escapes being choked by her own daughter, who also has black eyes. Sam is tied to a chair and confronted by Rufus and Jo, quoting latin. Then the “demons” splash Sam with holy water and pour salt down his throat. Sam realizes that something is wrong…his captors think that he is the one who is demon possessed, yet it is they who look like demons. Back at the church, Ellen tells Dean that Jo called her a black-eyed bitch and they too realize that they are no demons.

War, one of the 4 horsemen of the apocalypse, created the illusion of demons to turn the townspeople against each other. He boasts of this to captive Sam, then he makes Dean and Ellen appear like demons in the church, forcing them to flee for their lives when the survivors turned on them too.

Dean and Ellen work together to capture Rufus and Jo and convince them that there are no demons. After they do this, Sam is released and Sam and Dean go hunting for War as the townspeople launch another attack on each other. The Winchester find him as he is about drive off in his classic red Mustang. Unable to kill him, they cut his ring finger off and this dissipates the illusion just in time to prevent Ellen from being killed.

Later at a highway rest stop, Sam and Dean talk about the lack of trust between them. Sam suggests that he stops hunting for a while and Dean agrees. Sam takes his duffel bag from the impala and hitches a ride with a truck driver, leaving Dean behind.
The end.

Lucifer is on earth and the apocalypse has begun. Sam is racked by guilt because he caused it, Dean is stoic, smart-mouthed and trying to treat it like any other hunt. But the world-ending war still awaits two of it’s major players: Lucifer who needs a human vessel, and Dean, destined to kill Lucifer but refusing to corporate with the angels.

The Winchesters survive Lucifer’s blazing escape because they were transported into an airplane flying above. Not questioning this seeming miracle, they seek Castiel’s help, but soon learn that he is dead, killed by an archangel. They are forced to lay low at a motel trying to figure out their next move while avoiding both demons and angels who want to nab Dean for opposing reasons.

Chuck, the prophet, sends a message to them, via an obsessed fangirl, that there is a weapon on earth that can kill Lucifer…the archangel Michael’s sword. They recruit Bobby to help them decipher Chuck’s clues, but Bobby is demon-possessed and leads demon Meg right to them. When Meg orders Bobby to kill Dean, he manages to wrest control from the demon just long enough to stab himself, instead. The Winchesters prevail in the ensuing fight and escape with a gravely injured Bobby in tow.

The brothers leave Bobby in a hospital emergency room, then head to upstate NY and John Winchester’s storage locker where they believe Michael’s sword is located. There, dead demons and live angels, including Zachariah, await them. Zachariah tells them that Michael’s sword is none other than Dean himself. He is chosen to be Michael’s vessel. When Dean refuses the “honor”, Zachariah begins to torture him and his brother. Then, the once-dead Castiel materializes armed with an angel-killing dagger and kills two of his fellow angels and forces Zachariah to flee.

Soon afterwards, Lucifer finds a willing host…a grief-stricken man, angry at God over the murder of his family, Bobby is told he is unlikely to walk again, and Dean tells Sam that his choice of demon Ruby over him, his own brother, had been unforgivable and that he no longer trusts him.
The end.

The Apocalypse is nigh and Dean has been called into service by the angels. He is taken away mid-argument with Bobby to what looks like a luxurious palace to await his instructions.

Back in middle America, Sam and Ruby are on the hunt for Lilith. They have captured her “chef” and Sam uses his mojo to torture Lilith’s location out of her. Fearing her impending death, the demon returns control to the terrified woman who it possessed, causing Sam to have second thoughts. But Ruby reminds him that he needs her demon blood to kill Lilith and there is no more time left.

Dean learns from the angel Zachariah that his job is not to stop the Apocalypse, but to end it after it begins, that it is his brother who will begin the Apocalypse by killing Lilith, the final seal. He attempts to leave but finds that the palace has turned into a gilded prison. Dean appeals to Castiel who defies his orders and helps Dean escape. Castiel takes Dean to the prophet Chuck who tells them Sam’s location, then he transports Dean there, staying behind to hold off the archangel.

Dean arrives at the abandoned convert before the seal is broken, but Ruby sees him and bars the doors against him so he cannot reach Sam. His muffled shouts and pounding at the door goes unheeded as Sam proceeds to kill Lilith at the alter.

Afterwards, Ruby laughs in triumph and tells Sam that he has done exactly what he was destined for. Sam is flabbergasted as she takes pride in her role in manipulating him to make all the “right” choices to fulfill that destiny. Sam angrily tries to kill her, but has no more mojo left. Then Dean breaks through the door armed with the demon-killing knife. Sam grabs Ruby and holds her as Dean stabbed her to death.

Then the convent floor becomes awash in a blaze of light as Lucifer’s prison door opens.
The end.

As the night gives way to daylight Dean wakes from a fitful sleep to find Castiel sitting beside him on the bed. Unbeknownst to Dean, Sam had crept out of the motel room in the dead of the night to meet Ruby. Castiel tells Dean, “you have to stop it” then touches Dean's forehead. A dazed Dean suddenly finds himself lying on a wooden sidewalk bench outside in the daylight.

Forced to move by a beat cop, Dean walks to a nearby diner where he strikes up conversation with the dark haired young man sitting next to him. Dean learns that he is in Lawrence, Kansas and that the date is 1973. When someone calls out the name Winchester both Dean and the dark-haired man turn around. When the caller goes up to John, Dean becomes aware that the young man next to him is none other than John Winchester, his own father.

John leaves the diner and Dean follows him to a car dealership where he convinces him to buy a 1967 impala instead of a VW bus. From there, Dean follows John to the home of Mary Campbell, Dean's own mother who John is currently dating. While spying on his soon-to-be parents during their date, Dean is confronted by Mary outside the diner. Mary engages Dean in physical combat and Dean is barely able to subdue her. In the struggle, he sees her bracelet of charms and realizes that his mother is a hunter like himself.

After their date was over and John drives away, Mary introduces Dean “Van Halen” to her parents (his grandparents), Samuel and Deeanna Campbell, also hunters. Dean learns from Samuel that there are possible demonic omens in the area. Horning in on his grandfather's hunt, Dean discovers that the yellow-eyed demon is in Lawrence and making deals with young people. Using the colt which he “borrows” from Daniel Elkins, Dean attempts to kill the yellow-eyed demon now (in the past, that is) in order to save his mother from dying in the fire in the future. But the demon escapes by holding Mary hostage and Dean is unable to get off a shot. Later Dean confesses to his grandfather who he really is and why it is so important to kill the demon only to be laughed at by the yellow-eyed demon, himself, now occupying his grandfather's body. The demon kills Samuel Campbell and his wife, then goes looking for Mary who had run off to be with John Winchester after the hostage incident.

When demon Samuel find Mary, he kills John and forces Mary to make a deal with him so she could have John back in exchange for an invitation into her home 10 years in the future. Dean arrives after the demon sealed the deal with a kiss. The demon escapes before Dean can fire the colt and Dean was unable to prevent the tragic future that his mother faces.

Castiel appears and takes a devastated Dean back into the present. Back in the motel room, Castiel tells Dean he could not have changed the past. He sent him back to learn the truth about his brother Sam. Then he tells Dean that Sam is on “a dangerous path” and that Dean needs to stop him or they will.
The end.

Dean Winchester is back! His soul has been pulled from the pits of hell and pushed back into his body with such force that the trees surrounding his burial site have been flattened. After dragging himself out of his own grave, he finds that his body has been completely healed of all mortal wounds, but there is a new scar on his shoulder, a scar that looks like a hand print.

When Dean knocks on Bobby's door, Bobby' reaction is disbelief and kill-first-ask-questions later. He is convinced only after Dean demonstrates that a cut from a silver knife doesn't poison and holy water in the face doesn't burn.

When Dean and Bobby shows up at Sam's motel room, Sam's reaction to Dean's appearance is disbelief and kill-first-ask-questions later. He is convinced only when Bobby tells him it's really him and Dean says “I look fantastic”.

After Sam denies having anything to do with Dean's resurrection, though he did try and fail, they visit a psychic friend of Bobby's to get answers. But the entity cannot be viewed with human eyes and the psychic is blinded for her efforts.

Next, the Winchester question some demons in the area, but they too have no answers and are running scared. Sam wants to kill the demons, but Dean says no they are outnumbered. Dean wants to summon the thing that pulled him from hell, but Sam says no it's too dangerous.

Sam sneaks off to confront the demons with an all-new Ruby as companion. Deans goes off to summon the entity with good old Bobby at his side. Sam succeeds and sends the demon to hell with his bare hands and a new found psychic ability. Dean summons the entity, but cannot kill it despite his best efforts. This being now occupying the body of a man, claims to be a angel of the lord. He tell Dean he has been resurrected to perform a mission for God.
The end.

There is just over one day left before Dean goes to hell and the Winchesters are at Bobby's trying to find a way out of Dean's deal. Bobby uses a tuning device to find Lilith, the demon who holds Dean's contract. But they have no way to kill the demon, so Sam secretly goes to Bobby's barn and summons Ruby. But Ruby refuses to give Sam her demon-killer knife. Instead, she tries to persuade him to use his dormant demonic powers. Dean interrupts them and deliberately starts a fight with Ruby. Dean uses the fight to snag Ruby's knife and trap her in a “devil’s trap”. Then the brothers leave and head to New Harmony, Indiana to go after Lilith with their newly acquired demon-killer weapon. They are followed by Bobby, who refused to be left behind in this fight.

On the road, Dean discovers that he can see the true face of demons when a demon-possessed cop pulls the impala over. With only 5 hours left, Dean's closeness to hell has given him this ability and he uses it to locate demons protecting Lilith in New Harmony. Ruby shows up and the three of them sneak into the house where Lilith is, then separate to find her. Sam finds the child but she is no longer possessed by Lilith and time has run out for Dean. Fleeing a hellhound, all three lock themselves in a room that Dean protects with goofa dust. Ruby persuades Sam to give her the knife and he is about to when Dean looks at her and declares that she is not Ruby. Sam tries to stab her but her powers are too great and she pins him to the wall. Lilith-Ruby opens the door and lets in the hellhounds to attack Dean. Then she turns on Sam and tries to fry him with with her demonic power, but strangely it does not work on Sam and she backs away from him in fright. Sam advances and tries to kill her but she flees Ruby's body. He goes over to his brother and breaks down crying as he stoops to hold Dean's torn and lifeless body in his arms. Dean Winchester is dead. In Dean's unblinking eyes we see a horrific scene of him in hell, impaled by hooks and chains and screaming for help.
The end.

Dean has only 15 days left and no way out of the contract. The brothers attempt to force a captured demon to tell them who holds Dean's contract, fails. After Sam exorcises the demon, he mentions a case in Erie, Pennsylvania where a man was killed by something that took out his liver. Dean is puzzled by Sam's turnabout, but agrees to go on the hunt. In Erie, they learn that the killer is an old nemesis of their Dad's, Doc Benton, a 19th century physician, obsessed with immortality, who steals body parts to replace his own. About to close in on the doctor, the hunt is interrupted when Bobby calls and tells Dean that he knows where Bella is. Dean wants to drop everything and go. Sam refuses and admits that he wants to learn Doc Benton's secret. Sam thinks his immortality formula is a way out of the deal. An argument ensues. Dean goes off to find Bella and the colt. Sam stays behind to find the doc.

In Erie, Pennsylanvia, Sam finds Doc Benton's backwoods cabin, steals the doc's journal, rescues a woman, and is confronted by Doc Benton. In Canaan, Vermont, Dean befriends Rufus, a former hunter and recluse, learns from him about Bella's past, then confronts Bella in her hotel room. In Erie, Sam fights off the doc and runs over him with his rented jeep. In Canaan, Dean searches Bella's belongings but doesn't find the colt, threatens to kill her, then changes his mind and exits. A phone call later and Sam tells Dean of his success in finding the doc's journal and Dean tells Sam of his failure to find the colt. This conversation is abruptly cut off when Sam is chloroformed and kidnapped by Doc Benton.

Sam wakes up to find himself strapped to an operating table with his eyes taped wide open. Doc Benton is about to remove one of his eyes, when he is shot multiple times by Dean. Dean then stabs him through the heart with a knife dipped in chloroform, sedating the unkillable doc. With Sam's reluctant help, Dean buries the doctor and his journal in a refrigerator turned makeshift coffin that is chained shut.

That night, Bella sneaks into the Winchester's motel room and shoots into their twin beds, but the brothers are long gone. The phone rings and Dean is on the other end. He tells Bella he knows she made a deal with a demon and that her 10 years were up, tonight. She begs for help. He says it's too late. Bella then reveals the name of the demon holding his contract. It is Lilith, Sam's nemesis. The call ends and we hear the sound of a baying hound while a teary-faced Bella stares out the motel room window.
The end.

The brothers take on a case in Milan, Ohio where people are killing themselves after getting phone calls from deceased loved ones. Disguised as company execs, they visit the telephone company branch office to trace a century old telephone number that showed up on one victim’s caller-id. Stewey, a sloppy, porn-addicted technician, reluctantly came up with a list of people called, but was unable to find where the number came from. Their own EMF check on Thomas Edison’s “spirit” phone in a museum also came up empty. Then Dean’s cellphone rings and he hears his dad voice on the other end before the call drops off. Dean thinks the call is genuine, but Sam is skeptical. That night, “John Winchester” calls again and tells Dean about a way to get out of his demon deal.

The next day, Sam heads out to rescue a young victim and Dean goes to the house that “dad” directed him to. Sam discovers that the “spirit” caller is a “crocada”, a soul-eater that lives in filth and says “come to me” to it’s victims, and calls Dean to meet him at the phone company. Sam confronts Stewey, the phone tech, but is captured when the real “crocada”, Steve, another phone company employee, hits him from behind. He learns he never actually spoke to Dean and that Dean was sent into another trap by the “crocada”. Sam manages to free himself and kills the crocada after a struggle. Dean, in turn, fights a man he thinks is a demon, then realizes his error and stops. Both brothers return to the motel a little worse for the wear, but alive and well. The end.