A twelve-year-old boy named Thomas Miller is the school troublemaker. He gets into fights, causes distractions in class, and tells lies. Thomas is seen at the beginning of the movie fighting another student until Principal Hampton intervenes. He is next seen in class with Mrs. Bleckner, in which he is assigned detention for goofing off.

While in detention, Mrs. Bleckner decides to leave to get her nails polished and her hair done. Thomas sneaks out and goes to the library to read and talk with other students instead. On his way to the library, he overhears an unseen figure discussing a plot to kidnap the president's daughter on a cellphone. Petrified by this thought, Thomas leaves.

Thomas then encounters an FBI agent named Randal. Randal claims to be involved with researching the case and trying to stop it. Thomas explains what happened and the two go and meet up with Albert, a fellow FBI Agent.

Randal, Albert, and Thomas all perceive that the kidnapper is planning on striking during the school dance that weekend. Thomas invites his best friend Jackie to go with him, but Principal Hampton and Mrs. Bleckner kick them out. They sneak in anyway and continue to search in order to discover the kidnapper.

Albert joins Thomas and Jackie in their search. Meanwhile, Randal goes looking on his own and happens to come across the unseen kidnapper. The kidnapper fearing being exposed, attacks Randal using a broom. The kidnapper drags him away.

Albert, Thomas and Jackie continue to search the dance floor in search of clues but none arise. However, there is a suspicious feeling lurking about. Meanwhile, Mrs. Bleckner is seen walking down the hall, patrolling as a hall monitor; where she hears banging on the door of the janitor's closet. Now suspicious, she opens the closet door and finds Randal inside, bound and gagged. She sets him free, and the two go to stop the janitor, who Randal reveals to be the villain.

Mrs. Bleckner and Randal arrive and run onto the dance floor. Mrs. Bleckner exclaims that the janitor is the kidnapper and that she just saved Randal's life. The janitor is outraged at this, grabs the president's daughter, and flees. Albert, Randal, Thomas, and Jackie chase him down and follow him onto a helicopter. Thomas jumps onto it, sneaks up on the janitor and knocking him out, before putting the helicopter on autopilot. A SWAT team and the national guard appear with military-style assault rifles and get Thomas and the president's Daughter to safety. Thomas is worshipped as a hero and everyone throws a huge celebration.

• Spy School at IMDb