Amestris has just witnessed a successful coup by the military to overturn the Fuhrer and has reestablished the Parliament as the main system of government. As part of the restructuring process, the government is aiding rural areas, helping them advance in technology and other areas. New cities are springing up during this revitalization period, and in the suburban town of East Grinstead, Amestris High has been created, the first government-sanctioned public high school in the country. As military officials start to resign, Amestris High seems the perfect place to let them start over.
Maes Hughes, Roy Mustang, and his group of subordinates find themselves assigned to Amestris High by the military even after they resign their positions. Edward Elric, fresh from a position as State Alchemist under General Basque Grand, similarly finds that the military still controls his life even after he quits. The quiet life with his newly restored brother, Alphonse, seems to slip from his grasp as he is thrust into a new military-run institution complete with rules, student housing, and a rigid administration.
Former military officials and local students flock to the new school in hopes of getting a secure job or an improved education. But with hormones running rampant, students that aren't even human, and a teaching staff that disregards the rules almost as much as the students, learning seems to be the least of everyone's worries.