Zachariah and Company plant a vision in Chuck's head to draw Dean to his dad's old storage unit, thinking the Michael Sword is there. Zach tells Dean he is the sword, a vessel for Michael to take over and lead the war against Lucifer. Dean says no, no matter how Zach tries to force him to say yes. Castiel shows up to interrupt the torture, punish Zach's nameless goons for backing the wrong horse, and make Zach fix the boys and go away. He carves a sigil into Sam and Dean's ribs--pretty much unremovable, I'm thinking--that will hide them from angel and demon alike.
And along the way, he implies that he was put together, and Sam and Dean were pulled out of Lucifer's entrance site, by someone more powerful. But who?
Here are the prevailing theories, in order of my preference, with some arguments for and/or against each:
Is God back in the building? He would certainly have the power to yank the boys up into an airplane without anyone noticing, to instantly detox Sam, to take the millions of pieces of...Chunky Soup and put them back into Castiel. Also, Cas is pretty darned motivated all of a sudden. Gone is all the indecision he battled last season, the questions over what was right and what was wrong. He didn't hesitate to kill and banish and even order Zachariah around, to which Zach responded pretty quickly.
Castiel never really veered from his belief in God, though he felt as if he was. I can see God rewarding him for his loyalty by making him his emissary. We can also tap into other stories that lay out "rules" for what God and Satan can and can't do in the battle for humanity: Generally, God is hampered by free will. So his (or her!) direct interference with events is forbidden, or restricted. I can see the writers employing that concept here.
2. Some other high-up being
According to Wikipedia, Michael is the only archangel named in the Bible as recognized by both Christians and Jews. But some books of the Bible also name Gabriel and Raphael. So if Zachariah is banking on Michael, maybe one of them is opposing him, again using Castiel as his emissary. He would be higher on the totem pole, which might explain Zachariah's immediate capitulation.
Another argument for this is that if God is the one in charge now, that pretty much puts an end to Zachariah's plan, doesn't it? He was basing everything on God having left the building, and he knows the punishment for defying God's wishes is death. That would put a big hole in continuity of narrative. But if it's Gabriel or Raphael, Zach could be sufficiently cowed by them to stop his immediate actions, but not the long-term ones.
This was actually my first thought when we saw the light, that Michael didn't approve of Zachariah's Guantanamo methods. It's still a possibility. Maybe he intends to lead the war, but wants Dean to be a truly willing vessel, not a coerced one, or he plans to find another vessel. Or maybe he doesn't intend to come to earth, and wants Castiel to guide the boys in the war, instead.
4. Someone we haven't seen/thought of yet
Not much to say about that, because if we haven't seen them or thought of them, it's hard to predict them. Any ideas?
5. Lucifer and/or Castiel himself
One of my friends doesn't trust Cas at all. She's very suspicious about how he came back, and thinks maybe Lucifer put him back together. After all, Castiel has fallen, hasn't he? Or has he? We know he at least has fewer powers--Misha keeps saying he's been fired/laid off, and is becoming less angelic. Falling means a death sentence, so if he's fallen, why would God or one of the more powerful angels use him?
Lucifer would definitely like to prevent Michael from taking over Dean, and he's seems to be pretty good at emotional coercion. He could have convinced Cas to work for him, or manipulated him into it without Cas realizing.
It's also possible that whoever put Castiel back together isn't giving him orders, but that Castiel is operating on his own, taking advantage of his second chance to do what he feels is right.
It also occurs to me that the stuff the writers and actors feed us isn't always accurate. After all, Kripke said (I think in a preseason  issue of Supernatural magazine) they were going to use different actresses for Ruby, and that wasn't really the case long-term.
Is the Castiel Debate taking the place of the Ruby Debate? Will we question Castiel's goodness and loyalties all the way through the season? And if so, will we be thrilled or disappointed at the outcome? Whatever it turns out to be, this mystery has the potential to be my favorite one of the season, and I can't wait for tomorrow!
So, which do you think it is? Or do you have another theory I didn't list? Tell us in the comments!
Screencaps courtesy 13-bullets.com.