Posted May 18, 2016
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Make it a management game, similar to either Majesty or Dungeon Keeper.
You are the one running the school. You can adjust the curriculum (signs/alchemy/combat), you can assign teachers, and you can send the alumni out to do their jobs. Add an overarching plot that moves forward independent of your actions (think Uplink) and let the players figure out what is happening and how they can affect such plot.
Have the plot be about someone attempting to destroy the schools. You will be getting reports of other schools being attacked, and you will have the option of sending reinforcements to other schools, or people to help the attacked schools. Reinforcing a school will mean your school will be more vulnerable, and won't be able to function at full efficiency, but it will slow down the menace, helping other schools means you may get new people in yours, either teachers who no longer have a place to teach, students that may or may not need more lessons, or even captives for intelligence.
Hm, I seem to be describing an X-Com game. That does sound delicious indeed.