The writers for Supernatural have always been pretty good at dealing with consequences, so this episode was not unexpected. There had to be some fallout from the arrival of the apocalypse and Sam's role in it. What could have been a rather predictable set of circumstances, however, takes a delicious turn.
A number of people predicted that Sam was supposed to be the vessel for Lucifer, and had the Brothers Winchester not been removed from the spot where Lucifer rose from the pit, he might well have been. Instead, Lucifer is tracking Sam down so he can manipulate Sam into consenting to possession. That is unlikely to end well.
After all, if Dean is fated to be Michael's vessel, and Sam is fated to be Lucifer's vessel, then the story is rushing towards the kind of brother vs. brother conflict that has been in the cards since the second season. I doubt it will play out quite that way, since the writers have successfully taken the story in other directions before, but it does seem to suggest that Sam and Dean will be separated for a while longer.
That, in and of itself, is a good indication of how well the writers have thought things through. As the Antichrist Superstar, it makes perfect sense that Sam would be the vessel for Lucifer. That's pretty much the way the Book of Revelation has it going down. Sam has even been killed and brought back to life. A lot of the details are different, but it all hangs together pretty well.
I also like the fact that Lucifer does not carry himself as an evil villain. This is very much a portrayal in the John Milton tradition. Lucifer sees himself as someone willing to do what must be done, so that things can be the way they should be. It would be easy to assume that this implies that Lucifer is somehow good, but only those not paying attention could assume that. Lucifer is simply rationalizing his actions and putting a pleasant face on cold and calculated manipulation.
What is intentional, and even more obvious in this episode, is the portrayal of the angels as just as deluded. Raphael boldly declares that God is dead, but soon enough reveals that this is simply what the angels have come to assume after being left to their own devices for more than a century. The clear implication is that God always knew that this is how the apocalypse would have to play out. What Raphael believes is not necessarily true, and both Castiel and Dean admit, in the end, that they still believe God is out there.
Pairing up Dean and Castiel was a stroke of genius, especially since it has been in the cards for a while. There is a lot of fan service going on in the episode for the Dean/Castiel crowd, but it is well done and doesn't fell forced. Misha Collins knocks it out of the park as the angel in a strange land. His expression in the brothel was priceless!
For all that it was mostly about Dean's desire to forget about missing Sam and struggling with his solitude (his little speech at the end was total self-deception), the trip to the brothel also brought up another important point. While Castiel did -rebel-, it wasn't necessarily against God. It was against the corrupted command structure of the angels, who themselves have all fallen into the Lucifer trap. If anything, Castiel may be the only truly loyal angel left in the bunch.
What makes all of this such a powerful story is the character development over the course of the entire series. Sam began the series as the one connected to humanity, positive and spiritually strong. Now he is the one isolating himself more and more, falling into the darkness. Dean, on the other hand, began as the atheist with little time for the spiritual side of the war. Now he's running around with an angel looking for God. Yet, through it all, they are completely recognizable as the Sam and Dean we've always known.
As I said in the review for the premiere, the only drawback right now is the show's own success. The show has managed to survive this long by a surprising surge in the ratings, and that might force the show to continue past its intended end date. Just that possibility means that the fate of the Brothers Winchester is almost certainly known: they would have to live for the series to continue. Considering that the most potent aspect of the story is the possibility that one or both of the brothers might die to save the world, that steals a lot of thunder from the story. Hopefully, the competition will be just strong enough to depress the ratings enough to make this the final season. Sure, it's an odd thing to hope, but why would anything pertaining to Supernatural be typical?