Chuck comes home to find his dad stressing out. He says he keeps wondering why they'd let Chuck go on missions without the Intersect since he's such an ordinary guy. Chuck says he's not, and the CIA thinks he's special. They believe in him. Bakula agrees that Chuck's special and throws a knife at his face. Chuck flashes and catches it before it hits him. Bakula's all, "I was right!" And then stresses about how he worked so hard to get the first Intersect out. Chuck's like, "Dad, knife. Face. What if you were wrong?!" Bakula says he's never wrong. Which, you know, I totally believe. Bakula tells him that the Intersect can have a negative effect on the brain, which he didn't tell him since he didn't know he'd downloaded the new one. Chuck tells him he left, again, and he's living without him, just like he taught them to do. Bakula leaves, saying he can't stay and watch his son die. In the courtyard, Ellie asks him if he's leaving without saying goodbye. She says she just missed him and wanted to make sure he's okay. He tells her not worry and he won't be gone as long this time. They hug and she plants something on him. He leaves, and she calls Justin. "I did it. I planted the tracer." He tells her it's nice work and it guarantees her father's protection.
Bakula's already at his cabin (so he's close), where he pulls out a hidden giant computer and goes to work. Chuck's looking up his dad on the CIA computer at home when Sarah comes in and asks where he is. She thinks he must have had a better reason than finding out Chuck's the Intersect, since he loves Chuck. Chuck says he knows his dad loves him, but he doesn't know him or understand that for the first time, his life means something. Bakula keeps working on his giant computer, which also involves taking apart his watch an inserting a piece of it into the computer. Sarah asks if Chuck told his dad that, but he didn't, of course, and he doesn't know where he lives. Luckily for Chuck, Sarah figured it out, being an amazing spy and all. Bakula keeps on working on his project. He says something worked. Then, at some point, his computer's tell him there's a perimeter breach. He puts the watch back together and hides the computer as guys in military suits approach. Justin tells one of them, via telephone, not to leave until they have "it." Whatever it is.
Chuck and Sarah show up, and he says he's going in there to talk, but doesn't need her. Though, if he doesn't come back in twenty minutes, she should come save him. Seriously? Who leaves their significant other in the car for twenty minutes. Inside, the military guys are threatening Bakula when Chuck knocks. They pull him inside too, and he's like, "Give me a break." Sarah sits happily outside, as the bad guys release gas in the cabin so it will look like an accident. Military guys asks Bakula where "the Governor" is, and then figure out it's his watch. Bakula apologizes to Chuck, since he didn't want to drag him into anything. Chuck tells him he came her to show him he's special, but he thinks he'll just have to show him. He flashes and unties himself from the chair they had him tied into and starts kicking some ass. The bad guys can't fire guns because of the gas. Bakula somehow gets free, too, and joins the fighting. Sarah hears the commotion and gets out of the car. Fighting continues, and when a knife's headed toward Chuck's face, Sarah shows up to throw an ax and block it. Then she knocks out another guy, and Bakula asks if she has the Intersect too. Chuck: "No, Dad. That's all her." Then, to Sarah: "Hi, honey." Okay, they're adorable.