Chuck, never learning from his past, chooses to tell Morgan, but not Sarah, about his dream that Shaw's alive. Lucky for him (and us), Morgan can't keep a secret and tells Sarah almost immediately. She wonders why he didn't tell her and they start their search for Shaw, which leads them to the penthouse that Sarah's all too familiar with. Meanwhile, Bakula shows up after getting coded messages in classified ads from Ellie (hey, something has to keep newspapers in business, right?), and suspects that Chuck's still working as a spy. Chuck lies, and then admits he's just a part-time CIA analyst, and then Bakula follows him to Shaw's penthouse and ends up saving him from Justin, who broke in to steal what was in Shaw's safe. While Justin was busy trying to kill Chuck, he also was standing up Chuck's sister, who was meeting with him to discuss her father, since she'd lured him to Burbank inadvertently.
Justin ultimately gives Ellie a spy mission, which is to plant a tracer on her dad (she does) just before he heads back to his Ted Kaczynski cabin in the woods. The bad guys get there after Bakula runs some mysterious tests. They ask him for the Governor, and then Chuck shows up and gets held hostage, too. Ultimately, though, he flashes and saves his dad (with a little help from Sarah, no Intersect required). Then his dad tells him about the Governor: It's a watch he wears to regulate the Intersect and keep it from killing his brain, basically. He's going to make one for Chuck, too. When Casey's tasked by Chuck to keep an eye on Ellie, she understandably gets more suspicious of him, and when she finds him in her apartment, she can't use the gun Justin gave her and instead knocks him out with a frying pan. She runs off with Justin, who locks her in his office at what she thinks is CIA headquarters (it's not). And then, in the end, after everyone thought Chuck was wrong about Shaw being alive, we see Shaw download the Intersect into his own head. That's interesting how the Ring had the Intersect this entire time, but wasn't using it. How very conveniently stupid.
Also: Some stuff happens about Jeffster! and their music, and Big Mike becomes their mentor. But it's stupid and doesn't matter all that much, so I'll save it for the weecap.
There are a few things Chuck would like us to know: Read the recaps, because basically the entire season matters. We open on a cabin in the woods, as Bakula sharpens a knife when there's a knock at the door. It's just his newspaper (which, two things: It's delivered all the way out there? And: it knocks?). He notices an ad for a 1978 Chevelle in the classifieds, and translates whatever it says into: "Dad, I really need to see you. Please send me your address. Love, Ellie." He smiles and then we see her interpreting her own classified, which says: "I'll be in touch. Miss you, Dad." Awesome's making a smoothie in the kitchen, so Ellie uses the opportunity of his blending to call Justin and set up a meet in a few minutes.
Chuck calls Morgan and tells him about his dream that Shaw's alive. He says he hasn't told Sarah, and he knows relationships are important, but he just needs Morgan to meet him in ten minutes. Sarah comes in and asks what relationship. Chuck lies badly that it was about Morgan and Anna and how torn-up he is. Chuck changes the subject to how good Sarah looks and smells. Then he leaves. In Morgan's "office," Chuck says he saw Shaw die, and Morgan asks if he checked his pulse. Chuck says he fell into a river, and Morgan's like, "Of course he's alive! Haven't you ever seen a John Carpenter movie?" He is the best nerd ever. Morgan says that if Shaw's alive, he knows all about Sarah, Chuck, and ... Morgan. He starts to worry, and asks Chuck if he'll let him into Castle, where he left something. Chuck makes him swear this is their secret and also tells him not to touch anything.
The next scene is, of course, him touching everything. He's putting on a bullet-proof vest when Sarah finds him and asks if Chuck's up to something. He tells her he wouldn't know, but she sees through it and gets a little threatening with him. Chuck's back at the Buy More looking at a picture of Shaw on his phone. Casey comes up behind him and asks if he's reviewing pictures of people he killed. "I do that too from time to time." Morgan comes up in a big, puffy winter coat and confesses to Chuck that he told Sarah, because she's very persuasive. Chuck asks if that's a bullet-proof vest and Morgan asks if Chuck's tie is bullet-proof. But Morgan's saved not by his brilliant avoidance, but because Chuck sees his dad come into the store. He freaks out, and tells Morgan his dad still thinks he quit the CIA the night of Ellie's wedding and doesn't know about Intersect 2.0 in his brain. He didn't want to tell him after his dad spent so much time getting the first Intersect out of his head. Bakula greets him, and Chuck acts awkward and asks him what he's doing here. Bakula says he was checking to see if everything's okay because he got a message from Ellie. Then he sees Casey and points out that he wouldn't work here if the Intersect project was disbanded. Sarah comes up behind him, and Bakula asks Chuck why his handler's here. Chuck says they're boyfriend-girlfriend now. Bakula asks him to tell him he's no longer in the CIA. Chuck says the Intersect's out of his head and he's no longer a spy. He turns over the iPhone with Shaw's picture on it, and says, "You know me. I wouldn't lie." He looks way more comfortable doing so than Sarah does listening to it. Cake opening credits.