As the upgraded Intersect, Chuck trains to become a full-fledged spy but hits rock bottom when he flunks out of spy school and loses Sarah in the process. Meanwhile, Morgan comes home from Benihana School to help Chuck get over Sarah.

Chuck must use his relationship with Awesome to protect a visiting dictator, Premier Goya, who is the target of an assassination. While Awesome is excited about the prospect of being a spy, Chuck is more concerned about Awesome and Ellie's safety.