We open by reliving those last few moments of last season, when Chuck uploaded the new Intersect and learned kung-fu. Everyone was shocked, including Chuck. Typing tells us it's "Six Months Later. Prague." Chuck's being manhandled by some thugs, one who addresses him with a thick accent, calling him "Agent Carmichael." Chuck: "Call me Charles." The guy laughs, but Chuck goes on that the guy, Uri, has a case that belongs to Chuck's boss and he'd like it back, please. Uri mocks him, all, "What if I don't, Guy With No Gun?!" General Redhead tells Chuck, through the earpiece he's wearing, that they have a lock on the case, which is in the room with Chuck. Uri mocks him some more, so Chuck flashes and jumps up and does some kung-fu to get Uri's gun. He points it at them and asks for the case back. General Redhead tells Chuck to shoot him, and even Uri says, "Shoot me." But Chuck doesn't. Instead he just goes kung-fu on Uri and his two or three goons. He knocks them all out and then General Redhead asks him what's going on since his heart rate just spiked. He replies into his watch that he's fine. He got punched in the face and it's throbbing, but otherwise he's good.
He takes the case and runs. General Redhead tells him to get to a roof, because the chopper's inbound and the guys are after him. He runs to the roof, but she says the chopper's too far out, so he should zipline to the next building. He protests, but she tells him it's in the intersect. He pulls off his belt, but tells her he's not flashing. She tells him to flash, but he says if she stresses him out, it's never going to work. I think he's going to have to learn to deal with stress if he's going to keep up this spy thing. She tells him to flash a few more times, and he tries to tell himself to as well, but it doesn't work. Just then, Uri and his guys come out and point their guns at Chuck. General Redhead walks out with a megaphone and lights come up. She says, "That's all, Frank. Terminate the simulation." She tells Chuck to come down now.
On the ground, General Redhead asks Chuck why he didn't shoot Uri, and he says that even though it was a simulation, they were very close to each other and he's just not comfortable with the whole shooting people thing. General Redhead tells him this isn't working out. Chuck knows they've had setbacks, but he swears he can be a great spy. She says they spent millions to get him up and running as the new Intersect Agent, but it's not working. Chuck thinks maybe his dad can help, but General Redhead says the problem isn't with the computer; it's with Chuck. She says Intersect 2.0 was designed to go into a real spy, like Bryce Larkin (even in death, he's overshadowing Chuck), someone who can control his feelings. She fires Chuck. When he tries to stop her, saying she has no idea what he gave up for this, she says, "Frank," and one of her own thugs knocks Chuck out with some sort of stun gun.
As he falls to the ground, he flashes back to uploading the Intersect while Bryce died and we hear Casey tell him to tell his sister he's going on a last-minute trip to Europe for six weeks. Chuck asks where they're really going, and then we see Chuck and Casey having the conversation "Six Months Earlier" (so ... right after the finale, for the easily confused). Casey says they're going to a training facility for Chuck to learn how to use the new Intersect, to become a superspy. Chuck asks Sarah if she's heard he's going to be trained to be a real spy. She heard, but doesn't look happy about it. He asks what's the matter, and she says if he does this, he's going to be a spy for the rest of his life and everything will be a new mission and a new identity, and he won't be the same person. He says that's a great thing, but she says they could run away together and never look back. She has some money saved up, and would have to get them new identities. She tells him to go to the training facility in Prague, but to meet her at the Nedrazi train station in three weeks and she'll figure it all out. He asks what she's saying, and she says she wants to be a real person again. With him. She says this is what he wants, right, and then asks if he'll run away with her. He says yeah, and they both smile.
Back in the present, Ellie and Awesome are asking Chuck what happened, where Sarah is. He just sits there zoning out, but finally says he lost her, the girl of his dreams, and it was all his fault. Ellie suggest picking up the phone and calling her, since she's sure she misses him too. Cut to Sarah swimming in a cute white bikini. When she gets out of the water, her phone rings, and an accented guy sitting next to the pool hands her the phone, calling her "my dear." As if a spy would just leave her phone lying out next to her new mission/boyfriend. She looks at the phone, with Chuck's picture on it and throws it into the pool. On the other end, Chuck says, "Pick up Sarah." But then the phone goes dark in the pool. Opening credits. No Anna, but it looks like the rest of the cast is back: Chuck, Sarah, Morgan, Awesome, Big Mike, Jeffster!, with Ellie and Casey.
Then commercials, including one I must recap because it's sort of a spin-off of this show (great idea, NBC (and Honda)!). Ellie and Awesome are driving through the foresty countryside in a silver car. They tell each other "good morning" sweetly, and then Ellie says the Winter Classic was a great idea, but the two of them driving back to L.A. like this is ... Morgan pops up from the back seat and says, "Awesome!" Ellie and Awesome both scream in shock that Morgan's been hiding in there. Morgan joins in the screaming as they drive by a horse. Then they're unloading his stuff (close-up of the Honda logo) out in the countryside, and he says it's not a big deal; he'll wait for a bus. He has a luge and a bunch of other wintry stuff like ice skates. He says it will all be valuable sports memorabilia after he gets Olympic athletes to sign. But he doesn't know what he'll do with three passes to the Olympics. Awesome gets all excited, even saying, "Babe, people ski with guns! It's awesome!" Ellie says Vancouver's over 2,000 miles away, and Awesome and Morgan both look sad. But she finishes with, "We're gonna need some snacks." They all hug and then drive off, discussing which superpowers they'd have. Ellie chooses to disappear, Awesome chooses to stop time so he can have an eternity with Ellie. Morgan chooses X-ray vision and practically burns a hole in the back of Ellie's seat with his eyes. Awesome screams at him. Honda Accord Crosstour.
The next day, Chuck wakes up, puts on slippers and a robe and heads to the kitchen. Ellie and Awesome are eating breakfast in their scrubs. She greets him with a good morning, and he grabs a barrel of cheesy puff balls from the top of the fridge. They ask him how he's feeling, but he mostly ignores him and heads to the couch. He sits and eats the puff balls, and we get a montage (to Kenny Rogers's "Just Dropped In") of his feet putting on the slippers, him grabbing the robe, and him eating the cheese puffs as his facial hair gets longer and longer. In other words: He's in a funk. When the montage ends, Ellie wakes a bearded Chuck who's sleeping on the couch. She tells him that if he won't talk to her, there's someone else. Morgan pops into Chuck's line of vision, and Chuck grabs his face and sits up, asking if it's really him. Morgan says he's visiting for a few days, Hawaii's awesome, and he's flying through the ranks at Benihana. Chuck says he's proud of him and they should get together soon, but he passes out before he finishes talking. Morgan tells Ellie and Awesome it's worse than he thought. Ellie tries to force him to get up and do something today, but then tells everyone to leave and they all go as she mutters they'll leave him with h