At Castle, General Redhead scolds Sarah for losing Jill, so that now they not only don't know where Orion is, but they have a Fulcrum agent who knows all of their secrets (she hardly knows all of them, since she doesn't even know Chuck's the Intersect, but who am I to argue with a U.S. general?) running free. She asks where Chuck is now, and Sarah says he's on his way to the Buy More. Casey asks for permission to drop the twerp into a deep, dark hole. I think he's joking, but General Redhead surprises us all when she says, "Granted." At first I thought she was playing along with Casey, but then she continues: "It's over. The Human Intersect Project has become too hard to control." She can't afford to wonder anymore if this team or Chuck is a liability. Sarah asks what she's saying, so she says she's shutting down the project and putting Chuck into lockdown. He'll be taken to Washington and put into a secure facility, once and for all. Casey: "Operation Moron is over?" I can't tell if he's sad or not, which is I guess what makes him so good, but it makes me mad. Sarah says that Chuck won't go down without a fight, but General Redhead says that's why they're sending Sarah (her exact words: "Chuck trusts you. He thinks that you'd never betray him. Use that.") to tell him they found his father, who's at Castle. When he gets there, Casey will tranq him, and an extraction team will come to take him to Washington. Sarah looks at Casey, who just pulls out a tranq. She asks how he can just stand there and say nothing. He tells her General Redhead is right -- that the safest place for Chuck is underground. He asks her what she thinks will happen when Fulcrum finds Jill, anyway.
Chuck's at the Buy More, digging for Nerd Herder keys. Morgan walks by and tells Chuck he trusted the wrong person. Chuck's heading out with the keys, when Sarah walks in. She tells him they have good news, and he asks if it can wait, citing a "computer emergency." She tells him it's about his father. They found him. Chuck looks slightly skeptical, and asks "Why? How? Where is he?" She says one of their recon teams intercepted him as Fulcrum was moving him. She smiles and says he's back at the Castle, safe, and it's all over. Chuck laughs and almost cries, relieved. He tells Sarah he owes her an apology, because he was beginning to believe Jill was right: that the CIA would never let him go, that they'd always put their best interests ahead of his (well, of course they would; the CIA is not really in the business of looking out for one person but more about trying to stop larger threats to larger populations, but I digress...). He thanks her for always looking out for him, and she looks guilty.