The second season of Chuck contains 22 episodes and was originally aired from September 29, 2008 to April 27, 2009. The season continues to focus on Chuck's constant struggle to keep his spy life and real life apart as he becomes more accustomed to being a spy. More background on the Intersect project is revealed. Fulcrum, a hostile espionage organization that covets the Intersect, is featured more heavily as the season's main antagonist. Chuck and Sarah continue to grow closer, complicating their asset-handler relationship.
Chuck must prevent a menacing operative from obtaining a device that would ultimately lead to a new intersect. Meanwhile Chuck asks Sarah out on a real first date as Casey deals with a difficult assignment.
Chuck needs to go undercover to seduce a woman named Sasha Banachek, so an old school spy named Roan Montgomery is assigned as his mentor. Meanwhile, Captain Awesome finds himself in need of some relationship advice, and and turns to Morgan, and Lester faces his first problems as assistant manager.
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.
Chuck goes undercover at Sarah's 10-year High School reunion, where they meet the girl that tortured Sarah back in the old days.
Efficiency expert Emmett Milbarge pays the Buy More a visit to inspect the branch, while a global terrorist looks for Jeff. Chuck needs to socialize with Jeff to find out about his connection to the terrorist. Finally, it all comes down to video games and the prevention of World War III.
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 needs to acquire a Fulcrum agent list by solving several riddles left behind by Guy Lafleur. Meanwhile, Emmett tries to find out why Chuck is absent so often and goes after his colleagues to get the information.
After finding out that Jill is a Fulcrum agent, Chuck is ordered to use her to infiltrate Fulcrum. Meanwhile, Ellie is preparing the apartment for Thanksgiving and the arrival of Captain Awesome's parents. Morgan, Jeff and Lester are assigned to guard the store over Thanksgiving.
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 foils a plan to kill Tyler Martin, an international rock star. Chuck's night out with Tyler leads to trouble. Morgan holds a contest among his fellow employees.
Chuck and Sarah must pose as a happily married couple living in the suburbs, where they meet some interesting characters. Meanwhile, after his wife files for divorce, Big Mike goes on a rampage at work.
Chuck uses his burgeoning spy skills to help keep an eye on Anna for a heart sick Morgan. But their discovery leads to a chance that Anna's new boyfriend may be part of a dangerous gang. Meanwhile, Jeff and Lester nag Ellie into hiring their band, Jeffster!, to play at her wedding.
Chuck gets jealous when Sarah has to seduce a Fulcrum agent. Meanwhile, Jeff and Lester start looking for the "Buy More Babe" as a way of finding a new employee.
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
Chuck is contacted by the one person that can erase the Intersect from his mind. He starts having trust issues and doesn't know who to lean for help. Meanwhile, Buy More is having problems with the Buy More from Beverly Hills.
A female agent is sent to evaluate Sarah's performance, when Chuck's feelings for her are revealed. Meanwhile, Morgan, Jeff and Lester are trying to get invited to Captain Awesome's bachelor party.
Chuck's life seems to be coming together, his long-absent father has returned and he landed his dream job. Unfortunately for Chuck, neither turns out to be quite what he expected.
After Chuck's father Steve is kidnapped by Fulcrum, Chuck learns the only chance he has to find him is by putting his trust and life into the hands of the person he trusts the least—his ex-girlfriend Jill Roberts. Meanwhile, the Buy More team tries to sabotage Emmett’s corporate evaluation.
While Chuck and Sarah go on to rescue Steve they realize they have a chemistry together. Meanwhile Morgan becomes a pariah at the Buy More after mistakenly getting Emmett promoted.