During all that, Sam and Dean have been fighting their demons. A spare bomb would come in handy about now, wouldn't it? They finally off the newcomer demon and turn their attentions to Dr. Lab Coat. "Wait! I know things," he pleads. Dean, without taking his eyes off the demon, waves to Castiel. "Cass, go!" The angels flutter away. Dr. Lab Coat continues to plead for his life. "There's so much you don't know! You need me!" The logical thing to do would be keep the guy around and question him a bit, but then the Winchesters would know about the angel tablet and we can't have that. So Dean guts him with the demon knife, thus ensuring their ignorance for a few more episodes.
Castiel and Samandriel materialize near the Impala. "You're safe," Castiel tells the poor, doomed angel. "I'm taking you home." This fills Samandriel with dread rather than relief. He clutches at Castiel's sleeves and pleads with him not to take him back to Heaven. He confesses that he told Crowley things he shouldn't have. "He got to our coding," he says. "Secrets I didn't even know we had." Samandriel tells him about Naomi, but it's like the first time Castiel has heard the name. "They're controlling us, Castiel," says Samandriel.
Naomi yanks Castiel into her office. "Kill him!" she shouts. Castiel is confused. He wants to know why he saw her face, why he was so afraid. "What did you do to me?" he asks. She grabs him by his lapels and orders him to kill Samandriel. She shoves him away...
...and he's back on Earth again. His face looks pale and drawn, his eyes vacant. His sword slides from his sleeve into his hand, and then into Samandriel. Castiel calmly lowers the poor, doomed angel to the ground as the light goes out of him. Castiel seems without emotion until the whole awful thing is over. Then he looks quietly devastated to have killed the one angel he was trying to save.
"What did I just do?" he asks, suddenly back in Naomi's office. "You killed a traitor," she tells him. She says that Samandriel told Crowley about the angel tablet, but Castiel's guilt isn't assuaged. "I just killed one of our own to protect a tablet?" She reminds him of what the demon tablet can do, implying that the angel tablet would do much the same to them. Castiel should wonder why God would want to harm the angels, but he's not quite right in the head these days. "You're a hero," Naomi says. "And that's what I tell Sam and Dean?" he wonders.
The Winchesters find him holding Alfie's lifeless body. "You tell them Samandriel had been compromised," Naomi says. He echoes her words to Sam and Dean. She tells him to say he acted in self-defense, and so he does. Dean stares at him. "Cass, are you okay?" Blood runs from the corner of Castiel's eye like a tear. It's really quite an effective visual. "My vessel must have been damaged in the melee," he explains, sounding almost a bit... robotic. Naomi tells him to bring the body back to Heaven so she can see how far Crowley got. As if Samandriel hadn't already suffered enough, now he'll be subjected to what promises to be a gruesome autopsy. Castiel flutters away with Samandriel over Dean's protests.