Chuck faces his first moral dilemma as a spy. When agents Sarah and Casey refuse to help an unauthorized mission that is taking place in Chinatown by a top Chinese spy, Chuck is faced with a tough decision. Either go against the U.S. government and his friends, or do what he believes is right? Meanwhile, Morgan is caught in a dilemma of his own when Buy More forces him into a sales competition that could cost him his job.

Chuck has to return to Stanford University, the institute that expelled him, on homecoming weekend to help a former professor. Chuck finds out that his former professor is also a government operative who is being hunted out for a sensitive top-secret file. Chuck must use his past experiences to find his Professor's hidden secret, while at the same time discovering shocking secrets about his own life. More importantly, Chuck discovers the truth about his former friend, Bryce Larkin, the one who got him kicked out of Stanford. Meanwhile, Morgan has problems with the new assistant manager at Buy More.