As the 66 Seals needed to be broken, Lilith sent powerful demon Alastair to break another one by killing two Reapers. Alastair was opposed by hunters Sam and Dean Winchester with the help of psychic Pamela Barnes using astral projection in order to see the Reapers and save them. While Alastair succeeded in killing one Reaper with Death's Scythe, Sam and Dean managed to use their ghostly powers to free the other Reaper, Tessa before Alastair could kill her. In return, Tessa freed them and they fled before Alastair could react.
After Sam, Dean and Tessa teleport out of the funeral home where Alastair had been holding Tessa, Sam disappears, having been pulled back to his body by Pamela Barnes who is under attack by a demon. Not knowing where Sam is, Dean sends Tessa away to safety while he looks for Sam. However, Alastair appears before him, angry that Dean disrupted his plans. As Alastair advances on Dean, he is struck by a bolt of lighting and disappears. Castiel then appears and informs Dean that he and the angels have captured Alastair. Castiel explains that the funeral home is angel proofed, keeping him and the other angels from interfering while Alastair was inside, but he had called in the Winchesters, pretending to be Bobby so they'd deal with the threat from Alastair themselves. Castiel refuses to stop the people in the town from dying now that Alastair is no longer after the Reapers and refuses to explain why he saved Dean before leaving.
Following Alastair's capture, the angels imprison him in an old Enochian devil's trap in a warehouse in Cheyenne, Wyoming and attempt to learn from him who had murdered seven angels recently, believing it to be the demons and that Alastair, as a high-ranking demon, would know who did it. However, Alastair is a very powerful demon and a master of torture and is easily able to hold out against the angels. Needing information, the angels send Castiel and Uriel to recruit Dean, as Alastair's apprentice in Hell to torture the information out of Alastair, promoting Uriel over Castiel due to feeling that Castiel is getting too close to the Winchesters.
Returning from Pamela's funeral, Sam and Dean find Castiel and Uriel waiting for them and Dean is displeased to see them as Pamela died for their cause. Uriel explains that seven angels from their garrison have been murdered and they believe Alastair holds the answers to where to find the killer and how the killer is killing angels. The angels tell them that Alastair has been able to resist their torture and they came to Dean who trained under Alastair in Hell and is thus best suited to torture the information out of Alastair. Dean refuses, but Uriel tells him that they aren't giving him a choice before teleporting away with him and Castiel.
After Dean is gone with the angels, Sam calls in Ruby as he doesn't believe Dean is strong enough to break Alastair after what he went through in Hell but that Sam himself is. Ruby is able to use a tracking spell to find Alastair and feeds Sam some of her blood to make him strong enough to harm Alastair. He then leaves to find Dean, the angels and Alastair.
Taking Dean to the warehouse with Alastair, the angels demand Dean torture Alastair for them, but he refuses to do it. Uriel tells him it has to be done as angels are dying while Castiel tells Dean he knows its too much to ask, but they do have to ask it of him. Noticing that Castiel is following Uriel's orders and not the other way around this time, Dean gets Uriel to leave him to speak to Castiel alone and asks him why he's listening to Uriel. Castiel explains that the other angels feel he has been getting too close to Dean and is beginning to express emotion which can lead to doubt. Dean tells Castiel to tell his superiors that he doesn't want Dean torturing Alastair. Castiel tells him that he doesn't want it, but has been told its necessary. Dean tells Castiel that if Dean goes into the room and tortures Alastair, Castiel will not like what comes back out afterwards. Castiel just tells him that for what its worth, he'd give anything to not have Dean have to do this. Dean reluctantly agrees to help the angels torture Alastair.
Dean enters the room where Alastair is being held with a cart of torture implements, but Alastair is simply amused at the idea of Dean being sent to torture him. Dean gives Alastair a chance to tell him what he wants to know without the torture, but Alastair is unafraid at the idea of being tortured by Dean and taunts him by claiming that Dean is too scared to torture him and that Dean left a part of himself back in the Pit and he hopes that by Dean torturing him, the two parts of Dean will be reunited. When Dean tells Alastair he will be disappointed, Alastair comments that Dean hasn't disappointed him yet and figures that Dean wants revenge for all the torture that Alastair put him through. When that fails to get a reaction, he suggests that Dean should want revenge for all of the torture that Alastair put his father through, stunning Dean. Alastair tells Dean that he had John on his rack for a hundred years, similar to how he had Dean there and he made the same deal he did Dean, that he'd release John if he took up torturing in his place as he did Dean, but John never broke. Alastair has fun taunting Dean about how Dean broke in thirty years while John didn't break in a century and is then amused as Dean fills a syringe with holy water to begin his torture. Before starting, Dean tells Alastair that even in Hell, he could still dream and he always dreamt of the day that he could torture Alastair back and has some ideas of how to go about it.
Dean starts his torture by injecting Alastair with the holy water, but Alastair simply continues to taunt him. Dean then pours holy water over the demon-killing knife and stabs Alastair who tells Dean he carved Dean into a new animal and there's no going back. Dean just tells him that "maybe your right. But now its my turn to carve" and continues his torture with the knife as, unseen by either of them, Uriel loosens a screw on a pipe over the devil's trap and turns on the water, causing it to drip onto the chalk devil's trap and break it. When Dean goes to Alastair after carving into him with the knife, Alastair simply tells him its Dean's professionalism that he respects to Dean's disgust and Alastair's amusement. Dean starts repeatedly splashing Alastair in the face with holy water, demanding the name of the demon killing the angels, but Alastair continues to refuse to break.
As Dean tortures Alastair, Castiel waits in the next room where he is approached by the Fallen Angel Anna Milton. Anna asks why Castiel is allowing Dean to torture Alastair and points out that torturing doesn't seem like God's work. Anna suggests that this is not the will of God but rather one of their superiors. She tells Castiel that the father he loves wouldn't want this or ask it of Castiel. She goes on further to tell Castiel that torturing Alastair is not righteous and that he's feeling doubt now. Anna tells Castiel that the orders he is following are wrong and he knows it, but when she takes his hand and talks about them working together, he rejects her, telling her that she Fell and he's nothing like her. Castiel orders Anna to go and when he repeats the order, she reluctantly complies.
Despite Dean's best efforts to break him, Alastair simply continues to taunt Dean, telling him that he's not getting deep enough with his torture as he lacks the resources on Earth where reality is too concrete compared to Hell. Alastair tells Dean he has no idea how bad things in Hell really were for him and what Dean actually did for the demons, the true reason Lilith wanted him in the Pit. As Alastair refuses to shut up about what he's trying to tell him, Dean pours salt down Alastair's throat, making him choke. After recovering from that, Alastair continues on with what he was telling Dean, saying that it was actually supposed to be Dean's father, not Dean himself that did what the demons wanted. As Dean pours salt and holy water over the demon-killing knife, Alastair explains that he made the same deal to John that he did to Dean while John was in Hell: get off the rack and start torturing and Alastair would stop torturing him. However, while John didn't break, Dean did and when Dean started torturing in Hell, he broke the First Seal. When Dean refuses to believe him, Alastair quotes at him "and it is written that the first seal shall be broken when a righteous man sheds blood in hell. As he breaks, so shall it break." Alastair explains that they had to break the First Seal by breaking Dean before they could get to any of the others and tells Dean that when the demons bring on the Apocalypse, it will be all Dean's fault. Noticing the broken devil's trap, Alastair tells Dean he's not lying and that he wouldn't lie to Dean about this, calling it a religious sort of thing for him. Dean believes Alastair and tells him that even if the demons do win, Alastair won't be alive to see, but turns to find Alastair now free of his chains.
Taunting Dean about how the leaky pipe freed him, Alastair begins to beat on his former torturer and student, injuring Dean severely. Telling Dean he still has a lot to learn, Alastair prepares to kill him and take him back to Hell when Castiel intervenes and stabs him with the demon-killing knife. However, while the knife is able to harm Alastair, it is not powerful enough to kill the powerful demon who is more annoyed than hurt by Castiel's intervention. Castiel uses telekinesis to twist the knife, but it doesn't seriously harm Alastair who removes the knife and engages Castiel in a fight. Even weakened by Dean's torture, Alastair is stronger than Castiel and easily wins, impaling him on a piece of metal sticking out of the wall. Unable to kill Castiel, Alastair starts a spell to kick Castiel out of his vessel and send him back to Heaven. However, before he can complete the spell, Sam arrives and pins Alastair to a wall with his own telekinetic powers, releasing Castiel.
Sam demands answers from Alastair about who is killing the angels and how, but again Alastair refuses, asking Sam if Sam really thinks Alastair will tell him. Sam tells him he does think so and starts using his powers to torture Alastair who quickly breaks from the pain and tells Sam that the demons are not behind the angel murders and that if Lilith could kill angels, she wouldn't kill seven but "a hundred, a thousand." Sam realizes Alastair is telling the truth and stops the torture. Alastair taunts Sam to exorcise him if he can, but Sam tells Alastair that he's stronger than that now and can now kill demons. As Castiel watches on in shock, Sam uses his power against Alastair who writhes in pain, glowing gold as the power is used on him. Eventually, Sam kills both the helpless Alastair and his vessel with his powers.
With Alastair dead, Sam rushes the badly injured Dean to the hospital where he demands Castiel heal him. However, Castiel can't for some reason and leaves to further investigate the angel murders. Dean later asks Castiel if Alastair was telling the truth about Dean breaking the First Seal and Castiel confirms it. He tells Dean that as the one who brought on the Apocalypse, it falls to him to stop it, but Dean loses faith after hearing the truth and doesn't believe he can do it. It takes Zachariah coming to Earth and putting the Winchesters in a scenario where they have to do a hunt with no memory to show Dean that he's meant to be a hunter to get him back on track.
After Alastair reveals the demons weren't the killers, Castiel eventually discovers the broken devil's trap and realizes an angel must be behind the murders as no demon is powerful enough to overpower Castiel's devil's trap. Castiel confronts Uriel who admits to being the killer, having killed angels that wouldn't join him in freeing Lucifer. He had hoped that by freeing Alastair, the demon would kill Dean and escape, allowing Uriel to continue to pin the murders on the demons. During a fight between Castiel and Uriel, Anna kills Uriel, stopping the murders as the angels had wanted.
While Dean is still unaware at this point that Sam has started using his powers again, Castiel informs him of the truth at some point along with the fact that the angels don't know how Sam keeps getting stronger.
- This is the first time Sam uses his powers to kill a demon instead of exorcising it. However, Sam doesn't use that particular power often, only killing Alastair, Lilith and five demons when confronting Lucifer in Detroit to make a point.
- Sam is revealed to have been drinking demon blood in order to fuel his powers as shown when he takes in more than ever in order to be strong enough to harm Alastair.
- Castiel was initially intended to be killed by Alastair, but he was too popular with the fans and critics so the writers rewrote it so he didn't die.