Everything this show's been setting up starts to come together, when Chuck and Sarah find Chuck's dad, Scott Bakula. They bring him home, and he spouts crazy stuff about how he invented plasma TVs and touchscreen technology, but that a guy named Roark stole all of his ideas. Roark is an evil Bill Gates-type played by Chevy Chase. When Chuck flashes on a Roark flyer, he tells General Redhead, who sends him in to get a job there -- as himself: Stanford grad Chuck Bartowski. He gets the job, and when Sarah and Casey can't stop some big virus-infested software release, he steals the launch button from Roark. It's hilarious, because Lester and Jeff -- in the audience -- help Chuck, who's eventually knocked down by the young dweeb who hired him at Roark in the first place. All of this leads Chuck home, where he reads Orion's Intersect comic books, until his dad comes in and tells him if he sabotaged the Roark job for him, he shouldn't have. What Chuck quickly realizes is that Orion's Intersect schematics line up perfectly over Roark's headquarters. He tells Sarah and Casey Roark has an Intersect, but they don't believe it without proof. So, Chuck suits up in Casey's gear to go it alone. He gets caught by Casey, tranqs him, and heads to Roark.
Chuck's dad's already there, trying to get Chuck's job back. Chuck soon finds out his dad's much more than he seems, too. In fact, he's Orion, and he planned everything to go down this way. They go inside and find Intersect 2.0, which is supposed to remove the Intersect from Chuck's brain. But when they try to do it, Roark comes in to take Orion away to build super computers for him. He orders Chuck killed, but Chuck's dad says he'll do whatever Roark wants as long as Chuck lives. They let him live. Chuck's dad tells him that he was wrong about Chuck's handlers: He can trust them. Then they take him away. And, just when Ellie's coming around to not being mad at her dad, he's gone again. So Awesome makes her the pancakes for dinner that her dad promised the first time he left. Ellie tells Chuck she's sorry she wanted him to find their dad, because now she realizes he's never going to change and she doesn't need him. Chuck tells her not to count him out yet, and we close on a scene of Scott Bakula working on the Intersect. Who knew this show could do serious so well?
Previously: Chuck found out Orion could remove the Intersect. Then he met a computerized Orion, who gave him schematics for the new Intersect that Chuck needs to find to get his old life back. Chuck promised Ellie he'd find their dad to walk her down the aisle. With Sarah's help, he showed up at his dad's trailer at the end of the last episode. But we didn't see him (unless we watched the stupid preview).
Chuck and Sarah sit in the trailer while Chuck's dad digs in his fridge. His face is conveniently hidden in and then behind the fridge as Sarah and Chuck banter about how weird this is. She thinks his dad seemed happy to see him, but Chuck thinks it was more surprise. Also, the last time Chuck saw his dad, he was sort of crazy. His dad walks up and hands Sarah and Chuck their coffee, and it's Scott Bakula. He and Chuck catch up a little bit. Chuck tells him he went to Stanford, and his dad tells Sarah that Chuck was always a genius. Chuck tells his dad about Ellie, and her marriage to "an Awesome guy." He asks if Scott will walk her down the aisle. Bakula thinks it's not a good idea, but Chuck pushes, and tells Bakula he's seen what he can't do. He apologizes, but Bakula says it's okay, because he left, so now Chuck's mad. Chuck tells Scott he just wants him to come home for Ellie. Bakula likes that Chuck would do this; it makes him happy Chuck and Ellie at least had each other. He goes to pack to go with them. Chuck tells Sarah he's glad they found his dad for Ellie. Sarah points out it's for Chuck, too. Chuck says maybe he's not as crazy as he remembers. But then Scott comes in, looks out the trailer window and says maybe they should wait till dark, since the "rat bastards" are tracking his every move. Chuck and Sarah look at each other, all: "Nope. Still crazy."
At the apartment, Ellie's showing Awesome ties for him to wear at the rehearsal dinner. Chuck and Bakula walk in, and Chuck says hi. Ellie turns, says hi to Chuck quickly, and goes back into her nonstop tie talk. Then she realizes who she just saw, stops talking, turns around, and says nothing. Until... "Pancakes. You said you were going to make pancakes." She tears up and walks out of the room. Bakula's all, "That went well." Chuck hands him the luggage and leaves the room, giving Bakula and Awesome a chance to meet. Basically, Bakula hands Awesome his bag when Awesome reaches to shake his hand, then he compliments Awesome's "big TV." That's not a euphemism.