Since Chuck inadvertently download the top secret files of the US government into his brain, CIA and NSA have to assign agents to protect him and Chuck has to involve in some of their mission. Season 2 begins when Chuck gets used to with his spy life and has to prevent Colt from obtaining the Cipher.
What's the opposite of the sophomore slump? The sophmore surge? Sophomore surprise? Whatever you want to call it, "Chuck" is experiencing it -- big-time.