Nanotechnology inventor Dr. Albert Connors (MARTIN DONOVAN) has created an oil spill confinement process where pre-programmed "nano-bots" automatically and systematically devour their intended target. An international uber-villain, Brinkman (IAN McSHANE), and his henchman Francois Molay (ARNOLD VOSLOO), however, have for more grandiose and sinister plans for the bots. By using them to attack various missile installations, they'll be able to render the U.S. military helpless.
Accordingly, the CIA director (KEITH DAVID) realizes they have to take action to prevent that from occurring. Yet, they need an undercover agent to get close to Connors' teenage daughter, Natalie (HILARY DUFF), to spy on the inventor. Enter 15-year-old Cody Banks (FRANKIE MUNIZ), a junior agent with the CIA Development Program, Seattle division.
Having been trained in covert summer camps, Cody's secret agent status is secret to his parents (CYNTHIA STEVENSON & DANIEL ROBUCK) and younger brother, Alex (CONNOR WIDDOWS). He has no idea, however, how he's going to accomplish his task - getting Natalie to fall for him - since he's incredibly awkward around girls. Even so, he sets out to do just that and with the aid of adult agent Ronica Miles (ANGIE HARMON), Cody tries to win the girl, catch the villain and save the world.