Spy Classroom takes place in a world still shadowed by the Great War, when the devastating power of modern weapons pushed nations to rely on espionage instead of open conflict. In the Din Republic, spying has become one of the most important tools of statecraft, and Lily dreams of joining that hidden struggle and serving her country. Her enthusiasm is genuine, but her weak academic performance leaves her unsure whether she is really suited for the job.
That doubt begins to change when Lily is offered provisional graduation through a place on the spy team Lamplight, a strange opportunity she accepts despite knowing very little about it. When she arrives, she finds six other girls already waiting, each of them dealing with similar academic failures. Soon, the mysterious Klaus appears and gives them their first assignment: an "Impossible Mission" to infiltrate the Galgad Empire after only one month of training. With little time to prepare and no guarantee of success, Lily and the others must learn to trust one another, work under Klaus' guidance, and prove they can survive as spies.