Lisa's experience is partly based on that of Shannon Faulkner, the first woman admitted to the Citadel military academy in South Carolina.
During the scene where Bart is helping Lisa on The Eliminator after dark, one of the three classmates that stops and questions Bart is dressed in James Dean's iconic red jacket and blue jeans from Rebel Without a Cause (1955) (which is also what Fry from Futurama (1999) wears which is also made by Matt Groening).
The episode was written by Richard Appel, but the idea of Bart and Lisa attending a military academy had previously been pitched, and had been floating around since 1991. The idea had not yet been used as an episode plot, because the writers had not felt comfortable with taking Bart and Lisa to a strange place early in the series.
The spiky blond-haired boy, who runs towards the Eliminator while screaming, is a caricature of director Mike B. Anderson.
The title is a play on that of The Secret War of Harry Frigg (1968).