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.
Back at home, in his bedroom (which looks exactly like his room at Ellie and Awesome's, don't you think?), Chuck's reading when Bakula interrupts. He says he doesn't know how the Ring found him, but he does know what they wanted. He closes the blinds and fills Chuck in: The Governor watch governs the Intersect, basically protecting the brain from the electrical energy of it, which can lead to dementia or even death if not controlled. Bakula shows Chuck the inside of his watch, and says it governs his neural network, sort of like a pacemaker. He says he had to go back to his cabin to make sure one would work for the 2.0, and it will so he's going to make him one. He says Chuck's his son, and he downloaded it for the same reason he created the original: to help people. He wants to help Chuck be the man he wants to be. Chuck thanks him and they hug.