Despite the angel Zachariah's best efforts, Dean Winchester refused to consent to being the archangel Michael's vessel. Believing he was facing a literal firing, Zachariah was brooding in a bar when Michael approached him with a final chance to get Dean's consent: resurrect the Winchester's half-brother Adam Milligan and use him to draw out Dean. Zachariah eagerly agreed and set out to perform his task.
At the same time, unknown to the angels, Dean had given up after learning that God wouldn't help from Joshua and his encounter with the Whore of Babylon. After saying goodbye to Lisa Braeden, Dean prepared to go to say yes to the angels, but was found by his brother and the angel Castiel who knocked him out and took him to Bobby Singer's to keep an eye on him.
As Dean argues with Bobby and Sam over his plan to say Yes to Michael, Castiel senses something happening and disappears to a clearing in the woods where all of the trees are knocked over and a hand emerges from the ground. As Castiel goes to it, two angels attack him with their angel blades. Castiel quickly kills the angels and pulls what turns out to be a resurrected Adam Milligan from the ground.
After retrieving Adam, Castiel returns to Bobby's with the boy and the two angels' angel blades. Needing to hide Adam from any further angels, Castiel brands his ribs with the same symbols he used to hide Sam and Dean with. Adam wakes up when Castiel brands his ribs and surprises Sam and Dean by knowing who they are. He tells them that the angels warned him about them and demands to know where Zachariah is. Sam and Dean ask him to explain what happened to them and he does: while he was in his Heaven, the angels approached him and offered him the chance to save the world by becoming Michael's vessel to kill Lucifer. This surprises Dean as he's supposed to be Michael's vessel, not Adam. Castiel explains that as John Winchester's son, while he wouldn't be perfect, Adam would make a good vessel. Castiel believes that the angels wrongly assumed Dean would never say Yes and gave up on him but Sam believes that the whole thing is suspicious since the angels were so adamant about destiny and Dean being Michael's vessel. Adam tries to leave, but Sam stops him, telling him that the angels are lying to him. Adam doesn't believe it as they're angels and admits he knows how bad the fight could get, but believes that as long as it stops Lucifer its worth it. He tries to leave and derides his connection with Sam and Dean since he saw his father so little. Adam explains that the angels had promised to let him see his mother again if he agreed to be Michael's vessel, but Sam convinces him to give them a little time.
As a result of Adam and Dean both being willing to say Yes, Dean is locked in Bobby's Panic Room guarded by Castiel while Sam and Bobby keep watch over Adam. After seeing Adam considering an escape, Sam tries to convince him that their father was only trying to protect him by keeping him away from hunting, but Adam points out it didn't do any good since he was eaten by ghouls. Sam tells Adam that seeing John all year is worse than seeing him once a year, but Adam has had a hard life and tells Sam that anything from John would've been better than nothing. Despite Sam telling him that if he and Dean had known about Adam they would've protected him, Adam doesn't buy into the fact that they are a family. When Sam visits Dean in the panic room, Dean tells him he's not letting Adam say Yes, especially not after all of the people they've gotten killed over the years. Dean explains that he believes that Sam will consent to being Lucifer's vessel in the end, that he's not strong enough to say no and that Dean has to be there to stop him. Despite Sam's pleas for Dean not to believe that, Dean tells him that he can't help it but he does.
As Sam talks with Bobby, Castiel checks on Dean only to find he had drawn an angel banishing sigil on a cabinet door. Dean banishes Castiel and uses the opportunity to escape while the panic room door's open and nobody's guarding him. At the same time, while Sam goes out searching for Dean, Zachariah contacts Adam in his dreams and convinces him that Sam and Dean are not his family. Zachariah gets Adam to give up his location and transports him to the Green Room. At the same time, Dean approaches a street preacher and tells him to pray to the angels to let them know where he is. As the preacher starts to, Castiel finds Dean and knocks the preacher out. Castiel then drags Dean into an alley and beats him up in a rage due to the facts that, after everything him, Sam, and Bobby did, to stop Dean from saying yes to Michael was about to mean nothing. After everything that he done to try and stop The Apocalypse, everything he lost, him falling from heaven and losing his powers, was all for nothing, because Dean failed. Before knocking him out and bringing him back to Bobby's where Adam's disappearance has been discovered. Castiel and Sam lock Dean in the panic room again, but handcuff him to the bed this time.
In the Green Room, Adam asks when Zachariah will call Michael, but he reveals that Adam is actually just the bait to draw Dean out into the open so he can force Dean to say Yes. The angels knew that Sam and Dean's weakness was family and they'd both come for Adam if the angels had him. Adam is enraged by the revelation and Zachariah eventually has enough of him and makes him cough up blood.
Figuring out where Adam must've been taken, Castiel checks out the Green Room and finds it heavily protected by angels. Though Castiel and Bobby don't agree, Sam decides to release Dean to help them as Sam knows he and Castiel can't rescue Adam alone due to the number of angels guarding the Green Room. Dean points out that trap or not, he still intends to say Yes to Michael, but Sam has faith that when the time comes, Dean won't do it if given the chance. Arming themselves with the angel blades from the angels Castiel killed, Sam, Dean and Castiel leave Bobby's to rescue Adam.
Arriving at the old muffler factory in Van Nuys, California where the Green Room is located, Castiel tells them that the Green Room is guarded by five angels and they are too fast for him to just teleport in, grab Adam and get out. Castiel tells them he'll clear out the other angels so that Sam and Dean can rescue Adam and that while it may be suicide, he won't be around to see Dean fail to resist Michael as he doesn't have faith in Dean's ability to resist. As part of his plan, Castiel carves an angel banishing sigil into his chest with a box cutter and then covers it up with his shirt and trenchcoat. Castiel enters the warehouse where an angel guard attacks him. Castiel kills him with his angel blade and is then faced with all four remaining angels at once. Castiel drops his angel blade and taunts them into coming closer. Once they do, Castiel activates the angel banishing sigil carved into his chest, banishing the four enemy angels and himself.
With the way cleared by Castiel, Dean enters the Green Room where he finds Adam slumped on the floor in pain and no sign of Zachariah. Adam is surprised that Dean actually came for him and warns Dean that the whole thing is a trap. At that moment, Zachariah appears and asks Dean if he really thought it would be so easy. While Zachariah is distracted, Sam comes at him from behind with an angel blade, but Zachariah easily disarms him and throws Sam into a wall. Now having both Sam and Adam as leverage, Zachariah makes them start coughing up blood. Dean finally gives in and says Yes in exchange for Zachariah leaving Adam and Sam alone. Zachariah stops torturing them and smugly casts an Enochian spell to summon Michael. Looking at Sam and seeing his faith in him, Dean changes his mind and tells Zachariah that he has conditions first and that there are people's safety he has to guarantee before Dean lets Michael in. Zachariah tells Dean to make a list, but Dean tells him that his biggest condition is that Michael kill Zachariah. Zachariah doesn't believe that Michael will agree to that, thinking he's too important for Michael to kill, even for Dean's Yes. Dean tells Zachariah that he's expendable once Michael gets Dean's Yes so Michael will kill him if Dean demands it. Zachariah insists that Michael won't kill him anyway, but Dean tells him that "maybe not, but I will" before he pulls an angel blade and stabs it up through Zachariah's chin and through the top of his head, killing him.
With Zachariah dead, Dean quickly grabs Adam and Sam to make their way out of the Green Room as Michael descends to Earth. Sam and Dean manage to get out, but Michael remotely shuts the door before Adam can make it. Dean tries to go back in, but the doorknob is too hot. Michael fully descends and after he is gone, the Green Room, Adam and Zachariah's dead vessel are all gone.
With Zachariah and Adam gone, Sam and Dean begin to make their way back to Bobby's house. Along the way, they discuss Adam and Castiel's fates and doubt that they are both okay, but plan to find them again. Sam asks Dean about what changed his mind as he could tell that Dean really meant his Yes when he said it in the Green Room. Dean explains that in the moment when Michael was being summoned, he looked at Sam and thought about how Sam brought him to the Green Room despite the danger that he might say Yes and in the end, he couldn't let him down. The incident restores Dean's faith in their ability to stop the Apocalypse and for Sam to resist Lucifer and he tells Sam that they will screw destiny and do things their own way and together.
Sam and Dean later learn that Castiel survived his banishing himself and the other four angels and ended up on a fishing boat off the coast of Louisiana. However, banishing the angels and himself when he was so low on power causes Castiel to lose his remaining power and become human himself. He ultimately retains just enough angelic strength to resist Pestilence long enough to defeat him. He also informs them that following Adam's disappearance with the Green Room, he became Michael's vessel which they knew was a possibility.
As a consequence of becoming Michael's vessel, Adam is sent into Lucifer's Cage with the archangel when Sam sacrifices himself to send Lucifer back to Hell, taking Michael with them. After remaining in the Cage with Michael for a number of years, both Michael and Adam are set free when God opens every door in Hell as part of his plan to end the world. Having reached an understanding during their time in Hell, Adam remains the archangel's vessel after their escape, but Michael and Adam share control over Adam's body.
- This fight is the first time Sam and Dean wield angel blades against an enemy. In later seasons, they start wielding angel blades more frequently, though its mainly against demons once they learn that angel blades can kill demons too.
- Dean kills Zachariah in spite of Uriel stating that "only an angel can kill another angel." He later kills multiple other angels, including Lucifer and Sam kills Miriam and one of Arthur and Charlie's Captors. Other humans have since killed angels over the years as well.
- Dean killing Zachariah is the first time something other than an angel has killed another angel on the show.
- Though Dean avoids becoming Michael's vessel here, a little over eight years later, he consents to become the vessel of an alternate reality Michael in order to finally kill Lucifer, though with conditions that leave Dean in charge powered by Michael for the battle.
- In Season 14's Lebanon, the Winchesters encounter an alternate timeline Zachariah who never died here as a result of John Winchester disappearing in 2003. Zachariah is killed once again by Sam in similar circumstances to here, getting into Sam's face while taunting him and thus leaving himself in striking range of Sam's angel blade.