Castiel sits on a bench in a cemetery and contemplates everything that he's experienced, from the emergence of the first fish from the ocean to the land, to the end of the Apocalypse where he fought with Dean, Sam, and Bobby. Now he wonders if he's made the wrong choice.
Dean is driving in the Impala when Castiel appears in the seat next to him. They make small talk and then Castiel admits that he hasn't found Crowley yet, and doesn't know how the demon could have tricked him into believing he was dead. Dean says that he hasn't found anything yet, and tells Castiel that Sam is tracking a djinn in Omaha and Dean is heading there to help him. He asks Castiel if he'll call if he gets into real trouble, and Castiel teleports away without saying anything.
Castiel goes to meet Crowley, who is dissecting Eve. The demon has confirmed that Eve is still laying eggs, even though she's dead, and that any of her monsters in proximity suffer when Crowley electro-shocks her brain. Crowley complains that Castiel is distracted and let the Winchesters kill Eve, ruining their plans, and reminds him that they agreed that the angel wouldn't visit the brothers again.
Castiel remembers that he learned from the Winchesters how to stand up, and what to stand up for. When he was killed by Lucifer, Castiel was put back and realized what he had to do. He harrowed Sam from Lucifer's cage, confident that he could do it. However, he failed to return all of Sam, who went on a slaying rampage because he lacked a soul. However, even then he disregarded the clear warning that he was less than sure of what he was doing.
Crowley asks Castiel to kill the Winchesters, but Castiel tells him no and says not to worry. The demon doesn't believe it, but Castiel tells him to focus on finding Purgatory while he makes sure the Winchesters don't find him.
Bobby and Sam are interrogating one of Crowley's demon monster-hunters, Redd, who insists that Crowley is still dead. They don't believe him and torture him with holy water, but Redd doesn't break. Sam hands Bobby the demon-killing knife and jams it into Redd's thigh, and then they go out to talk to Dean in the kitchen. Dean tells them that he didn't tell Castiel anything, and insists that the angel is their friend. Bobby and Sam aren't so sure, and admit that if Castiel has gone bad then they're dealing with a Superman who has gone dark side. As they talk about finding Crowley and stop him from opening Purgatory, they're unaware that an invisible Castiel is watching them.
Castiel knows that they suspect, and is concerned about Dean, who is trying to be loyal to his friend.
Redd finally admits that he deals with the demon dispatch, Ellsworth. Castiel teleports to Ellsworth's home, where the demon equivalent of Bobby is coordinating demon-hunting efforts across the state via a blood chalice. To keep the brothers from finding and interrogating Ellsworth and getting to Crowley, who would kill them, Castiel kills Ellsworth and his minions.
Later, Bobby and the Winchesters arrive at Ellsworth's house and find it entirely cleaned out. An invisible Castiel watches them, having swept away the evidence.
After bringing Sam back, Castiel went to heaven and found Rachel and the other angels there to greet him. They believe that God brought Castiel back to lead them, and he tries to explain the concept of freedom to them. Raphael summoned him to pledge allegiance to him with the other angels, insisting that they'll free Lucifer and start the Apocalypse again. When Castiel defies him, Raphael blasts him out of his Heaven and tells him that he will kneel or die.
The trio finds nothing in Ellsworth’s house and realizes that it's too cool. Dean proposes that they have to call Castiel for help, insisting they owe the angel the benefit of the doubt. Sam gives in and he and Dean call Castiel, but the angel doesn't appear since he knew he couldn't answer their questions. As the trio starts to go, three of Crowley's master demons hunters attack. Castiel internally debates what to do, and finally intervenes, smiting the demons. Dean points out to the others that Castiel saved them, and Sam and Bobby apologize, admitting that they suspected Castiel of going to the dark side. Relieved that they trust him, Castiel tries to joke, inadvertently echoing their comment earlier about Superman going to the dark side.
Castiel confronts Crowley, who warns that the angel needs the Winchesters to believe in him so that Castiel can believe in himself. Angered, Castiel slams Crowley into a wall and warns that if he attacks the Winchesters again, he'll destroy everything they've worked for.
After Raphael defeated him, Castiel approached Dean, but refused to ruin his new life with Lisa and Ben. Crowley appeared to him and offered a deal. Confident that he was smarter and stronger, he went to Hell with Crowley to hear him out. There is a line of over a trillion people, and Crowley explains that he has renovated Hell so that even masochists get no relief, by having to stand in line forever. Castiel admits that he can either submit or die against Raphael, and Crowley proposes that Castiel gather an army of angels to defeat Raphael and his allies. When Castiel points out that would make him Lucifer, Crowley suggests that God brought Castiel back so that he could rule in Heaven. When Castiel points out that he doesn't have enough power, Crowley says that they can both draw on the monster souls in Purgatory. He wants to get Dean and Sam to help him find Purgatory, but Castiel refuses to involve them and Crowley says he'll get Samuel. They'll capture monsters, and the monsters will get them to Purgatory. For his efforts, Crowley will take half to secure his own position as king of Hell. When Castiel notes that they don't have enough time to find Purgatory before he has to face Raphael, Crowley offers him 50,000 souls as a loaner. The angel hesitates and Crowley says that deep down, Castiel believes that God wants him to lead.
Taking the deal, Castiel returns to Heaven and smites Raphael, and tells the angels to choose between him or his enemy.
Dean summons Castiel back to the Ellsworth house. When the angel arrives, they claim they had to bury the bodies and say they have a plan to track down Crowley. Castiel asks what it is, and they lure him into a circle of holy oil and ignite it. They accuse him of spying on them and Castiel can't bring himself to lie to them. The angel insists that he's doing it for all of them, and he needs the souls to stop Raphael and prevent the Apocalypse. He admits that he raised Sam from Perdition, and Sam notes that he didn't do a very good job of it. He then asks Castiel if he brought him back without a soul on purpose. Castiel denies it and says he had no choice, but Dean said that he had a choice and made the wrong one. He insists that they deal with what happens, but they don't deal with demons.
A wind picks up outside and a black demon cloud approaches the house. Dean says that they can fix it, but Castiel says that nothing is broken and tells them to run. The trio gets out and a few seconds later, Crowley enters the house. He extinguishes the holy flames and says that he won't harm the Winchesters, but it's always one's friends that hold one back. Crowley talks of the two of them being the new God and the new Devil, and Castiel tells him to get out. As Crowley goes out, he says that he's honest with himself and asks Castiel what he's willing to do.
Back at Bobby's house, Dean is trying to sleep when Castiel teleports in. He admits that Bobby got a few angel wards wrong, and says that he's here to make Dean understand. Castiel says that he's doing it because Dean taught him that freedom and free will matter. Dean tells him that free will doesn't mean one can do whatever he wants, and asks Castiel to do it as a friend. He explains that Castiel is like a brother to him, and he's asking the angel as a brother not to do what he's doing as a matter of trust. When Castiel asks what he'll do if he doesn't stop, Dean says he'll do what he can to stop him, angel or no angel. Castiel says that he's sorry and departs.
Back in the cemetery, Castiel finishes his story and begs God once last time for a sign to indicate if he's on the right path. He gets no response.