We see clips from Sam going into the cage, Castiel telling Dean that Sam's soul is missing, the revelation about Cas creating more souls for the war in Heaven through negating the sinking of the Titanic, Eve telling the boys she wants Crowley, and Crowley referring to having to clean up Cas's messes.
Cas is sitting outside saying he's been around a long time and seen many things -- when the first fish crawled out of the ooze, the Tower of Babel ("all 37 feet of it, which I guess was impressive at the time. But come on, dry dung can only be stacked so high."), Cain and Abel, David and Goliath, Sodom and Gomorrah. And he also remembers the most remarkable things, remarkable because they never came to pass, prevented by "two boys, an old drunk and one fallen angel." Of that latter grand story, "We ripped up the ending, and the rules, and destiny, leaving nothing but freedom and choice, which is all well and good except what if I made the wrong choice? How am I supposed to know? But I'm getting ahead of myself. Let me tell you my story. Let me tell you everything."
Next we see Dean driving down the road, and Castiel pops into the passenger seat to "check in." Both tell the other they haven't seen anything of "Satan Jr.", aka Crowley. It's painfully obvious that Cas is lying, and it's bothering Dean. But Dean's lying too. Poof, and Cas disappears. He shows up at some gruesome lab where Crowley is doing an autopsy on Eve with a side of torture to another monstery schmuck. Cas refers to Crowley saying Eve could open the door to Purgatory, and Crowley says that he believes she could have if she was still alive.
Crowley: "Your best change to get over the rainbow and the Winchesters killed her."
Crowley tells Cas that he's distracted and that makes Crowley nervous. Cas responds by saying he's holding up his end of their deal, but Crowley isn't happy Cas is still hanging with the Winchester boys.
"The stench of that Impala is all over your overcoat, angel."
Next we're back with Cas, telling his story. "We'd stopped Armageddon, but at a terrible cost." He reveals he's the one who brought Sam back from Hell and says he should have recognized the fact that he hadn't brought all of Sam back as a warning.
Crowley asks Cas to kill Sam and Dean or he'll do it. Cas tells him no and not to worry about them. Crowley begins listing all the people who didn't worry about the boys and died because of it -- Lucifer, Michael, Lilith, Alastair, Azazel.
Castiel: "Just find Purgatory. If you don't, we will both die again and again until the end of time. The Winchesters won't get to you."
When Dean reaches Bobby's, Sam and Bobby are questioning a monster named Red who's been hunting things for Crowley. They want to know where Crowley is, and Red isn't being cooperative. Dean tells Bobby and Sam about Cas popping in and how he fed him a line about being on some "crap monster hunt." They all hate the idea of Cas being in with Crowley, but they're being careful in case he is. Unknown to them, Castiel is in the room listening to their conversation about the fact that maybe he's gone dark side. Red finally reveals that he's never met Crowley, that he deals with The Dispatcher, a demon named Ellwsorth. Cas says that if there's a demon counterpart to Bobby Singer, Ellsworth would be it.
Knowing that Ellsworth and his demons would lead the Winchesters to Crowley, who'd tear their hearts out, Cas takes out Ellsworth and two other demons.
Cas: "I did it to protect the boys, or myself. I don't know anymore."
The boys and Bobby arrive at Ellsworth's place to find it empty. Cas laments the lies, the hiding and the sweeping away of evidence. "My motives used to be so pure." After supposedly saving Sam, Cas returned to Heaven. He says that there isn't one Heaven, that each soul creates its own paradise. He tells the angels they are free to choose what they want to do now. But he says those first weeks back were difficult. "Explaining freedom to angels is a lot like teaching poetry to fish." When he went to see Raphael, he asks whose Heaven he's in and Raphael says it's Ken Lay's and he's borrowing it. Raphael says that Castiel and all the angels will have to kneel to him, that he's going to free Lucifer and Michael and get the apocalypse back on the road.
Sam, Dean and Bobby try to call Cas for help, but he doesn't go to them because they have questions he doesn't want to answer. Then some demons show up and say, "Crowley says, 'Hi'." Cas shows up and smites the demons because the Winchesters and Bobby "are my friends. For a brief moment, I was me again." As they're talking, he slips up and reveals he's lying when he refers to going to the dark side, something the other three had mentioned when they didn't know he was there.
Castiel says that Raphael is stronger than him and he'd never stand a chance in a straight fight, so he went to Dean for help. Only when he thought about all Dean had sacrificed, he couldn't do it. That's when Crowley showed up wanting to make a deal.
"I'm an angel, you ass. I don't have a soul to sell."
Crowley shows Cas how he's redone hell. Everyone there is having to stand in an endless line, and when they get to the front they just come back to the end again. Crowley proposes an alliance in which each of them will get half the souls in Purgatory for his own use -- Cas for a civil war in Heaven, and Crowley to shore up his position as the king of Hell. He offers to float Cas a loan of 50,000 souls from the pit. Prideful, Cas accepts the deal and declares war on Raphael so he can avoid the apocalypse.
Back to the present, Bobby and the boys call Cas and when he arrives they trap him in the ring of fire and force him to tell the truth. Honestly, at this point I feel sorry for Cas because he seems like an angel who was in between a rock and a hard place. He might have made the wrong choices, but he had good intentions. But we all know what road is paved with good intentions. Dean tells him that he should have come to them for help.
Crowley shows up, and Cas tells Sam, Dean and Bobby to run, which they do. Crowley asks Cas what he's willing to do. Cas goes to Dean to try to explain, and Dean tells Cas that he's like a brother to him and asks him to stop this quest for Purgatory with Crowley. And if he doesn't, Dean says he'll do whatever he has to in order to stop him. Cas says he's sorry and disappears. Then we're back to Cas praying to God for a sign that he's on the right path. "Because if you don't, I'm going to do whatever I must." When no sign his offered, he drops his head.