"You have to choose," Naomi says. "Us, or them." She says "them," but she means "him." It wasn't random human beings she had to train Castiel to kill. It wasn't even the Winchesters. It was just Dean.
Cass-bot drops the All-Purpose Angel Sword and reaches down for the tablet. The tablet glows at his touch. As if traveling through whatever conduit existed between the real Castiel and Cass-bot, the glow reaches all the way to Heaven. Naomi shrinks from it. When the glow fades, Castiel has vanished from her office. She calls for him, but he doesn't appear to be at her beck and call anymore.
It's the real Castiel in the crypt who reaches out to touch Dean's ruined face. Dean cringes in anticipation of another blow, but the touch is a healing one. "I'm so sorry, Dean," Castiel says. "What the hell just happened?" Dean asks.
It would be lovely to find out what he says, but we still have to deal with Crowley. He's somewhat surprised to learn that Castiel is in the crypt. "So that's who's been poking my boys," he says, "and not in the sexy way." Well, as far as you know. Crowley has a notebook full of insults he'd like to try out, but Meg reminds him the episode is almost over. "I'm here for the stone with the funny scribbles on it," he says. "That's not gonna happen," Sam tells him. "Love it when you get all tough -- touches me right where my bathing suit goes," Crowley says. Sam's face goes, "Ew." Crowley whips out his All-Purpose Angel Sword. Instead of just killing Sam with a twist of his fingers, Crowley stands there and waits while Meg volunteers to cover Sam. "Go save your brother," she tells him. "And my unicorn." I just puked in my mouth a little. Instead of following Sam and getting the Angel Tablet for himself, Crowley would rather stick around and taunt Meg. He tells her the brothers plan to kill all the demons. Meg is totally okay with dying as long as it means Crowley goes, too. Crowley skewers her. In an odd editing choice, it happens out of frame.
In the crypt, Dean has just heard the details of how Naomi has been controlling Castiel since she got him out of Purgatory. "What broke the connection?" Dean asks. Um...you? You big dork. "I don't know," Castiel says. "I just know that I have to protect this tablet now." Castiel seems a bit confused still, so Dean prompts him: "From Naomi?" Castiel says, "Yes," then thinks about it some more and adds, "and from you." He flutters away, leaving Dean to gape at the spot where Castiel had stood. Before long, Sam comes to get him, telling him they need to get out of there.