Chuck sneaks away with former ex-girlfriend-turned-back-on-again-girlfriend Jill to the Buy More roof for a romantic picnic. Just as they're kissing, Chuck notices Casey's security camera has found them. He rants to the camera, appalled that he's being watched even in his private moments. As Chuck screams at the surveillance camera, Casey and Walker receive a new mission from General Beckman.
Beckman explains that a list of suspected double-agents (a.k.a. FULCRUM operatives) may be hidden in the hotel room of the late Dr. Guy Lafleur. Lafleur was working with Jill Roberts when he was killed in his hotel room; the room is now a sealed crime scene. Chuck, Sarah, and Casey will have to infiltrate the room past an FBI security phalanx, use Chuck's ability to flash and find the list, and then return safely without being detected.
Buy More's new Assistant Manager Emmett Milbarge grows suspicious of Chuck -- he seems to have far more out-of-office service calls than the other Nerd Herders. Morgan shows Chuck a computer chip circuit board he got illicitly from Canada that can copy anything digital: videogames, movies, files of all kinds.
For their mission to infiltrate the hotel room, Chuck and Sarah pose as a successful business man and his superhot call-girl escort. Jill sees Sarah dressed to the nines and grows jealous; Chuck tries to explain its all in the line of duty. Checking into the hotel, Chuck and Sarah sell their cover well and meet up with Casey, who explains there's a route into LaFleur's hotel room through the ventilation system.
As they clamber through the ducts, Chuck accidentally dials Jill on his mobile phone. She overhears him and Sarah struggling through the ducts, but thinks she's overhearing them having sex. Her jealousy rages.
Back at Buy More, Emmett is determined to bring Chuck down. He threatens Morgan with incriminating photos of him and Anna canoodling in the Home Theatre Room. Emmett's willing to show Morgan some mercy from discipline, but only if he will give up some dirt on his best friend Chuck. Morgan's not talking, so Emmett moves on to questioning Lester and Jeff, threatening to cancel their weekly poker game on company premises. Jeff tells him that Chuck is two-timing his girlfriend Sarah.
Searching the hotel room for the list of double-agents, Chuck flashes on an old wooden box, secured with an obscure puzzle lock. Chuck, Casey, and Sarah beat a hasty retreat as a FULCRUM assassin descends on the hotel room. Safely back in their hotel room, Chuck solves the box's puzzle lock. Inside, Sarah and Chuck find a mysterious metal cartridge. In a flash, it bursts, spraying them with a noxious purple powder. Thinking that they've been gassed, Casey leaves to get a containment unit while Chuck and Sarah run to the shower to decontaminate themselves. The powder turns out to be fruit punch mix. As Chuck and Sarah are drying off, Jill appears at the door and sees them in their underwear -- and is now more convinced than ever that the two are involved romantically.
Jill comes to the Buy More to confront Chuck, who explains to her why he and Sarah were coming out of the shower together. He tells her about the investigation of LaFleur's room and the puzzle they discovered -- and that the "gas" was actually fruit punch mix. Jill thinks she may know what Guy was trying to hide and that the punch mix may be a clue. Chuck blindfolds her and takes her to Castle, their spy compound underneath the Orange Orange shop. Casey and Sarah are mortified that Jill's in their secret location.
At Castle, Jill uses a mass spectrometer to analyze the fruit punch residue on the puzzle box. She determines it to be Hi-C Rootin' Raspberry. Chuck figures out that the Hi-C reference is musical. Casey, the former choir boy, belts out a credible high "C" note and the puzzle box opens to reveal a pair of antique opera glasses. Chuck looks through them, flashes, and determines that the glasses' handle is a key to secret lockbox.
Jill, Chuck, Casey, and Sarah all head to the opera house, where the troupe is rehearsing on stage. Chuck and Jill search Guy LaFleur's private spectator box. On the floor, Chuck spots a keyhole which matches the key from the opera glasses. The lock opens, revealing a secret compartment and another wooden box. Inside the box is a timer -- and another puzzle. Convinced that the box holds a bomb, Casey evacuates the opera house. Using their knowledge of classical music, Jill and Chuck solve the puzzle before the timer expires, revealing a flash memory drive.
General Beckman reports that the flash drive is protected with a super high-level of digital encryption; the agency's computers will try every possible code until they unlock the code.
Chuck and Jill take off to celebrate their success with an overnight getaway to the mountains. As they stop for gas, the FULCRUM assassin takes Jill hostage, demanding that Chuck turn over the flash drive in exchange for Jill. He instructs Chuck to meet him at the Opera house at midnight with the list or "the girl dies."
Chuck returns to Castle for help. But Casey refuses, explaining it's a matter of national security. Panicked, Chuck grabs the flash drive and runs for it. He stops by Buy More, then heads to the rendezvous at the opera house.
Jill and the assassin meet him onstage. As Casey and Sarah arrive with guns drawn, Chuck finds himself in the center of a standoff. Casey threatens to shoot everyone, but Chuck gives him a secret sign and then passes the data drive to the FULCRUM assassin, who promptly crushes it with his boot and the runs off. Outside, Chuck explains to an agitated Casey that, before turning it over to the FULCRUM agent, he made a copy of the list, using Morgan's ultra-powerful digital copying chip.
At Buy More, Emmett joins Morgan, Jeff, and Lester's card game, indulging in a few wine coolers. The next day, Morgan confronts a very hung over Emmett with tape of him from the night before -- when he was quite drunk and carrying on all over Big Mike's office. Emmett agrees to call off the witch hunt of Chuck.
As Chuck and Jill get down to some serious romantic celebration back at his place, Casey and Sarah agree not to watch from their surveillance post at Castle. They concentrate instead on the encrypted list of FULCRUM agents. As the faces and names of the double-agents come up one at a time, Casey and Sarah are shocked: Jill Roberts -- Chuck's Jill -- is among the double agents!
Casey and Sarah rush to Chuck's apartment only to discover that they've taken off, leaving Chuck's GPS tracking device behind. As they drive out of L.A., Chuck strokes Jill's hair. "Safe at last," he tells her.