At the same time, the angel Castiel attempted to hold off the archangel Raphael at the Prophet Chuck's house, resulting in Raphael smiting him for his interference. Upon being placed on a plane by an unknown source, the brothers returned to Chuck's house and they found it a wreck and were informed of Castiel's fate by Chuck who then sensed the arrival of Zachariah and his men. Zachariah tried to convince Dean to come with them, but Dean revealed an angel banishing sigil on the wall and banishes the three angels, giving credit to Castiel for teaching him that trick. Sam later creates hex bags to hide them from the angels and demons, having learned how to make them from Ruby.
Soon afterwards, Chuck contacted the Winchesters through Becky Rosen to give them a clue he received in a vision of the location of the Michael Sword, the weapon the archangel Michael used to defeat Lucifer the first time. The message tells them that its in a castle on a hill made of 42 dogs. While trying to figure out the message with Bobby Singer, Bobby mentions Dean's father and he realizes that his dad's lock-up is at Castle Storage at 42 Rover Hill which makes sense as the location. At that moment, Bobby reveals himself to be possessed by a demon and attacks Dean. Meg arrives with another demon, but after Bobby regains control long enough to stab himself and kill the demon inside him, the Winchesters overpower the other demons and Meg flees, but with the location of the Michael Sword. The two quickly rush to Castle Storage to get there before the demons.
Arriving at the lock-up, the Winchesters find the demons beat them there, but that Zachariah and his angels got there first and killed the demons. Zachariah reveals to Dean that Dean himself is the Michael Sword: he's Michael's vessel, his instrument on Earth. Zachariah tells Dean that its an honor that he's been chosen, but Dean refuses to be Michael's vessel. In response, Zachariah breaks Sam's leg. Zachariah tells Dean he's done screwing around and the angels need their general to lead them against Lucifer and his armies. When Dean questions how many humans will die in the crossfire, Zachariah easily admits that it will be several million, but states that the entire planet will die if Lucifer wins the war. Dean realizes that Michael needs his consent which is why Zachariah is explaining this rather than kidnapping him. Zachariah admits that's true and Dean once again refuses. Zachariah offers to heal Bobby's injuries if Dean says yes, but will prevent him from ever walking again if Dean refuses. Dean hesitates for a moment, but still says no. Zachariah then gives Dean stage-four stomach cancer and removes Sam's lungs, but Dean continues to refuse, telling Zachariah to just kill them. Zachariah refuses, telling them he's just getting started.
At that moment, Castiel suddenly returns and stabs one of Zachariah's men through the throat with an angel blade, killing him. He then fights the other angel, eventually overpowering him and killing him with a stab to the back with his angel blade. Zachariah is stunned to see Castiel as Raphael had killed him. Castiel implies that God resurrected him and put the Winchesters on the plane, which scares Zachariah as God had left Heaven long ago. Castiel orders Zachariah to put Sam and Dean back together and go and scared, Zachariah heals the two and departs.
After Zachariah is gone, Castiel tells Sam and Dean that they have to be more careful as Lucifer is circling his vessel at which point their hex bags won't be able to hide them from him. As a result, Castiel brands their ribs with sigils that hide them from the senses of all the angels in existence, including Lucifer and himself. After confirming that he was dead but not explaining his return, Castiel departs.
As a result of Castiel's rebellion, he becomes a Fallen Angel and starts losing his powers shortly after the standoff, starting with his healing abilities, keeping him from being able to heal Bobby. Convinced that God had resurrected him, Castiel begins a search for him using Dean's Amulet which can detect his presence. The angel Joshua later confirms that God did save the brothers from Lucifer and resurrect Castiel, but that He doesn't intend to do anymore to help feeling that this and the few other things He did to help directly are enough. God later brings Castiel back twice more, with his second overall resurrection being as a Seraphim.
Despite being forced to retreat at the end of the standoff, Zachariah continues his efforts to get Dean to say "Yes", taking him to the future, chasing the Winchesters across Heaven itself and resurrecting Adam Milligan before he's finally killed by Dean.