We pick up six months after Chuck uploaded the super, kung-fu fighting intersect in the season finale. He's being trained to be a super-spy, but when he fails, Agent Redhead fires him. This sends him into a funk of sleeping on the couch, growing a pervert beard, and eating barrels of cheese puffs. We find out in flashbacks that's because he gave up the chance to run away from the spy life to be with Sarah in order to take this spy job that he was just fired from. When he heads to Buy More for more cheese puffs, he finds out Sarah's still working at Orange Orange, and sees Casey coming out of Castle when he heads over. Casey tells him he and Sarah are about to leave for a new mission, so Chuck realizes it's time to find Sarah and talk about what happened.
Unfortunately, Chuck being Chuck and Chuck being Chuck, he finds them mid-mission and ends up disrupting it all, using his new skills to play Mexican guitar and punch the bad guy. When the bad guy finds his Buy More badge and goes to find him, he first finds -- and KILLS! -- Buster Bluth, then finds Chuck and Sarah. He locks them up in Mexico, but they break out and Chuck basically saves the day, since the guy was a Ring operative. So Agent Redhead turns Operation Bartowski back on, and everyone goes back to their old jobs and their apartments. Except Ellie and Awesome, who move into one across the courtyard and Chuck shacks up with Morgan (who failed at Benihana and Anna).
It all feels a lot like a reset, which I can accept, since they're probably trying to draw some new viewers. Oh, and there are some slight difference: Agent Redhead tells Sarah that Chuck's dangerous, so Sarah has to keep him emotionally stable. She says they used to protect Chuck from the world, but now that's switched up. Apparently that new Intersect put more than kung-fu and guitar skills in Chuck's head. Which makes you wonder why Agent Redhead would have fired him in the first place, unless she intentionally set the whole episode's actions into motion? Anyway, Chuck tries to pour his heart out to Sarah, and she shuts him down, saying he's a spy now and must keep his feelings hidden. Which feels once again like a reset, and one I'm less willing to accept without complaint. The episode ends with Chuck and Casey training (boxing each other after Chuck flashes). I missed this show.
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.