As Chuck is beginning to adapt to his new life as a spy, a doctor who could possibly "cure" Chuck is murdered. Chuck then begins a high-speed fight for his life, all while trying to decide which of his two new colleagues might be out to get him. Meanwhile, Chuck's sister Ellie invites Sarah to dinner to meet the family.
Chuck must learn to balance a real love life with his cover love life when he meets a charming young woman by the name of Lou. At the same time, his relationship with Sarah gets interesting when the duo must explain their sexual relations with Ellie and Captain Awesome on a double date. Meanwhile, there is trouble when someone is using truth poison in order to retrieve codes for nuclear facilities.
While coping with the realization that Sarah still has feelings for Bryce, Chuck must assume his toughest cover yet by going on a mission as Sarah's husband. The team must foil the plot of a politically connected counterfeiter, who may be endangering the lives of Anna, Morgan and Anna's parents. Both Morgan and Anna also find themselves in the cross hairs.
Two new characters are introduced, both of whom want to take the Intersect. One is a beautiful, young female enemy agent that works in the Pita Palace next to the Buy More, and the other is a handsome CIA agent who is posing as an undercover police detective investigating a theft at the Buy More who wants to take Chuck into his custody. The former quickly blows Chuck's cover, while the latter kidnaps him and makes him vanish from his former life.
Bryce Larkin returns to town with news about Fulcrum. They have hired a wealthy software magnate named Von Hayes to decrypt information on a stolen chip containing a refresh to the Intersect with highly classified information. Bryce and Sarah have to pose as a married couple at Von Hayes' dining party to steal back the chip, while Chuck has to pose as a waiter. Meanwhile, Morgan has an encounter with the Mighty Jocks at the Buy More.
At a BioScience conference, Chuck runs into Jill, his ex-girlfriend who broke up with him and later dated Bryce Larkin. He flashes on her boss, Guy Lafleur, who is suspected to be working on biochemical weapons. Chuck is ordered to reconnect with Jill in order to gain more information on Lafleur. Meanwhile, Emmett wants the staff to take CPR lessons including a test.
The team is assigned to survey the Global Launch Agency, when intel shows that someone might penetrate their security. During the surveillance someone intrudes the lab who turns out to be Casey's former sensei Ty Bennett. Meanwhile, Captain Awesome's perfect parents decide to pay Devon and Ellie a surprise visit to help them plan the wedding, and Emmett Milbarge introduces an "Employee of the Month" contest to the Buy More, but the employees start their own contest instead.
Sarah's father, a con artist, comes to meet her, revealing that he conned a Saudi Arabian sheik, Rajiv Amad, out of nearly a million dollars. The sheik turns out to be connected to terrorist fundings, so the General wants Sarah and Chuck to gain intel from Sarah's father, but things get complicated when Amad shows up. Anna wants to take her relationship with Morgan a step further and asks him to move in an apartment with her. Devon lends him some money to buy one, but instead, he buys a car.
Christmas Eve does not go as planned when an amateur criminal on the run from the police crashes into the Buy More and takes Chuck, Ellie, Awesome and the rest of the Buy More gang hostage. In order to protect Chuck’s cover and the safety of the other hostages, Sarah and Casey secretly go in to the store to remove Chuck, but the mission quickly falls apart when Chuck refuses to leave his friends and family behind.
Chuck, Sarah and Casey learn about a man called “Perseus” who is behind Fulcrum’s plans to build their own Intersect. While Sarah and Casey are sent to find Perseus, Chuck and Agent Cole Barker are forced to stay in a safety bunker. When the mission takes a dangerous turn, their orders to stay out of harm’s way go out the window. Meanwhile, Morgan tries to convince Anna that moving in with him would be a bad idea
When Awesome is mistaken for a super spy by the evil Sydney Price, Chuck must become his handler and show him the spy ropes. While on a mission for The Ring, they meet the mysterious Daniel Shaw. Meanwhile, Morgan gets promoted to assistant manager and must deal with Jeff and Lester's latest hijinks.
Chuck juggles his two lives as he trains new Nerd Herder Hannah and gets his very own asset who is caught up with The Ring. Chuck thinks he can handle his asset all on his own but Sarah and Casey feel the need to intercede. Meanwhile, Awesome must lie to Ellie when she starts to ask questions about Chuck and Morgan, Jeff and Lester do some recon work to learn more about Hannah.
Casey carries out a side mission for his old commanding officer James Keller that leads to him committing treason. When Chuck learns the dark truth about Col. Keller, he and Sarah set out to break Casey out of jail and clear his name. Meanwhile, Awesome's plan to keep Ellie out of danger gets more difficult when she gets her dream fellowship.
While in Europe, Sarah and Chuck realize they’re traveling on a train with Spanish spies. Even though they’re all alone, they decide to take on these rogue agents. Of course, this impromptu mission doesn’t go smoothly. Meanwhile, Beckman orders her newest “unlikely” spy team – John Casey and Morgan Grimes – to track down the missing couple.
Chuck and Sarah are assigned to train under Craig and Laura Turner, a married CIA team who, despite their impeccable record, hate one another. The Turners' stormy relationship forces Chuck and Sarah to wonder if they're doomed with the same fate. Meanwhile, Casey must train the newest member of the team Morgan.
Chuck struggles with disturbing dreams and now he believes his most recent dream predicts danger for a visiting head of state. General Beckman however, is unconvinced and assigns Chuck to meet with a CIA psychiatrist Dr. Leo Dreyfus. Meanwhile, Ellie gets surprising news and Anna returns to the Buy More to talk to Morgan.
Chuck and Sarah's romantic mission is canceled with the arrival of Hugo Panzer and Heather Chandler. But Chuck grows more interested when the manipulative Heather claims to know a secret about his mom. Meanwhile, as Morgan prepares the Buy More for a huge video game release, he gets a surprise from Big Mike.
Sarah takes dangerous measures to help Mary Bartowski bring down Alexei Volkoff, as Chuck worries that she may be getting in too deep. Sarah, though, must enlist the help of Chuck, Morgan and Casey to complete her undercover mission. Meanwhile, Ellie and Awesome are at odds over what to name the baby.
The mission to take down Volkoff reaches a dangerous new level, while big changes loom at home. As Sarah works to free Chuck’s mom, Chuck and Morgan embark on their own mission to take down Alexei Volkoff. Meanwhile, Casey bonds with his daughter, Alex, while Ellie tries to ease Awesome’s anxieties over fatherhood.
Chuck surprises Sarah with her old spy team, The C.A.T. Squad, leading to a mission in Rio. As The C.A.T. Squad works to settle a score with Augusto Gaez, old secrets and grudges come to light. Back at the Buy More, Morgan fends off the advances of Carina, a former flame and frisky member of The C.A.T Squad.
Valentine's Day is interrupted when Chuck and the team are sent on a mission to England to protect a reclusive young heiress, Vivian McArthur. Meanwhile, Casey gets an offer from the mysterious Jane Bentley. Back at home, Ellie and Awesome find an unlikely solution to a parenting problem, as Morgan ponders a big move.
Chuck is put in charge of a top-priority mission, but his leadership skills are pushed to the limit when there is a murder in Castle. Meanwhile, Awesome takes on a mission of his own when Ellie finds an alarming new hobby. Elsewhere, Morgan's leadership is also tested when his Buy More troops wage war against Large Mart.
A bad day gets worse when Sarah throws Chuck a surprising relationship curveball as the CIA orders Vivian Volkoff assassinated. In order to prove Vivian's innocence, Chuck must put his trust in a dangerous ally her father Alexei Volkoff. Meanwhile, Ellie suspects that her mother is interfering with the search into her father's past.
Chuck and Sarah’s wedding prep includes one final detail: ensuring that the mother-of-the-groom makes it to the ceremony alive. Meanwhile, Morgan’s responsibilities as Best Man include his most dangerous mission yet, as he faces Vivian Volkoff. Elsewhere, Ellie tends to the last details of the rehearsal dinner and seeks help from an unlikely source.
In the fifth series premiere, without the Intersect in his head or the support of the CIA, the world of espionage is a much more dangerous place for Chuck Bartowski and his team of freelance spies. To start, Carmichael Industries takes on a slick, rich thief named Jean Claude (guest star MARK HAMILL - Star Wars), and a conniving investor, Roger Bale (guest star CRAIG KILBORN - The Late Late Show with Craig Kilborn), who has stolen money from some of the world's most dangerous people. Meanwhile, Morgan helps Chuck with a special surprise for Sarah. Back in the Buy More, Jeff and Lester have taken things to another level with their latest scheme.
As the team takes on a missing persons case, Chuck and company struggle to establish themselves as Carmichael Industries in the face of a rival security firm led by the tough and efficient Gertrude Verbanski (recurring guest star CARRIE-ANNE MOSS The Matrix). Meanwhile, Morgan continues to adjust to the Intersect, while Chuck adjusts to being Morgans handler. Also, the Buy More finds an unlikely spokesperson to help motivate business. JEFF FAHEY (Lost, Grindhouse) and JUSTIN HARTLEY (Smallville) also guest star.
As the team is tasked with finding one of the CIA's "most wanted," Chuck fears that life as the Intersect may be going to Morgan's head and inflating his ego. Meanwhile Sarah helps Casey navigate his relationship with Gertrude (recurring guest star CARRIE-ANNE MOSS). Elsewhere, Captain Awesome makes a startling revelation about Jeff and Lester.
Chuck and Sarah go undercover at a Buy More convention to hunt down an assassin whose mission is to take down the new Intersect. Meanwhile, Morgan must deal with the consequences of having the Intersect. At the Buy More, Jeff begins to show a very different side of himself. DAVID KOECHNER (The Office, Anchorman: The Legend of Ron Burgundy) and CATHERINE DENT (The Shield) guest star.
A mission to track down a computer super virus leads Chuck to return to his roots as a hacker - and to call on his biggest competition, Gertrude Verbanksi (recurring guest star CARRIE-ANNE MOSS), for help. Elsewhere, a new Buy More employee (guest star DANNY PUDI – Community) complicates Jeff and Lester's friendship.
Chuck and Sarah race against time to take down a dangerous computer virus, pitting them against Robyn Cunnings (guest star REBECCA ROMIJN – X-Men, Ugly Betty), a ruthless spy who will stop at nothing to get what she needs. Meanwhile, Ellie and Awesome's date night takes a dangerous turn and Morgan is sent on a special mission to recover Chuck's P.A.N.T.S.
Chuck and Sarah discover who is behind the plot to destroy Carmichael Industries. Meanwhile, Ellie's plans for a perfect Christmas begin to come apart and, at the Buy More, Morgan and the gang must fend off angry customers as a computer virus threatens to ruin Christmas. Comic book legend STAN LEE guest stars. and, in return, gets makeover advice.
Sarah is forced to confront a secret from her past and feels she must do so alone, while Chuck urges her to let him help. When Sarah encounters her original handler, Kieran Ryker (guest star TIM DeKAY – White Collar), she fears that he will harm those closest to her, including her mom (guest star CHERYL LADD – Las Vegas, Charlie's Angels).
While Chuck and Sarah contemplate the next step for Carmichael Industries, Casey's forbidden love, Gertrude Verbanski (recurring guest star CARRIE-ANNE MOSS), walks back into his life with a questionable mission in South Beach. Meanwhile, Jeff's enhanced intelligence leads him and Lester to suspect that something unusual may be happening at the Buy More.
As Chuck and Sarah try to realize a new, safer future, Morgan's past as the Intersect sends them to Vail on one last mission, where they enlist the help of an unlikely source - the legendary BO DEREK (guest starring as herself - 10, Fashion House, Tommy Boy). Elsewhere, Jeff and Lester continue their own spy mission. Recurring guest star ANGUS MACFADYEN (Braveheart) appears as Nicholas Quinn.