Chuck is put up to an unusual task when a hot CIA woman requests help with a mission. Upon seeing her, Morgan asks Chuck to set her up with him. While working on the mission, Chuck discovers that a million dollar diamond being stashed in Malibu is being used to financially back terrorists.

Chuck encounters his first moral dilemma as a spy -- he must decide whether to side with the government and his friends or do what he thinks is right after Sarah and Casey refuse to help on a misson in Chinatown. Morgan faces his own dilemma when Buy More's sales competition may cost him his job.

Chuck runs into a fellow agent who is living a similar life to his own. He learns that the agent is a gadgets expert and debates whether or not to turn the agent over to Sarah and Casey or let the man escape his handlers. Meanwhile, Halloween, an important holiday for Chuck and Morgan, proves to be very different this year.

Chuck returns to Stanford, the university that expelled him, to help a former professor. The professor also happens to be a government operative who is being chased due to a top-secret file. Chuck must use his past knowledge to find the professor's secret and learns shocking information on Bryce Larkin, the person who got him expelled, along the way.

Meanwhile, new assistant manager Harry Tang insists on making things miserable for everyone at Buy More.

Chuck finds himself battling between his cover love life and real love life when he meets Lou, a beautiful girl interested in the real Chuck. At the same time, his relationship with Sarah heats up while on a double date with Ellie and Captain Awesome. Meanwhile, a poison specialist uses 'truth' poison to get into nuclear facilities.

After realizing that his relationship with Sarah had no chance of being real, Chuck decides to go out with a woman who is working at a local sandwich shop. However, things take a turn for the worse than the CIA begins to suspect that she may be involved in a smuggling operation.

Everyone is shocked to discover that Bryce Larkin is actually alive, but things become even more complicating when he escapes before answering any questions. Now, Chuck must figure out why his former friend betrayed him, though when he soon discovers something that shatters his confidence. Meanwhile, Morgan is placed in charge of Buy More’s holiday shopping operation.

Chuck and Sarah pose as a couple to stop a counterfeiting yachtsman with ties to political figures. Meanwhile, the staffers at Buy More attend the annual holiday party, which will see stricter guidelines from Big Mike.

Casey's old photojournalist flame, Ilsa, shows up with a fiancee. Unfortunately, it turns out that Ilsa was a spy all along....

Chuck finds a bug at the Buy More, cluing in Casey and Sarah that Fulcrum has knowledge of Chuck's connection to the Intersect. They have 48 hours to locate the bug's owner or Chuck will be taken into custody... permanently. Meanwhile, Chuck attempts to find Ellie's missing engagement ring.