>>720129484
The game never explains why they have guns or why they all have halos and can survive being shot at like its an ordinary occurrence. The real life reason is the writer wanted cute girls with cute guns doing cute things.
What you help save them from varies depending on which students you focus on. The president has disappeared mysteriously and (you) arrive to help fill the power vacuum as an external branch of this world's government. Different academies have their own political struggles internal and external.
For example, the first school you get introduced to proper: Abydos, is struggling with the fallout of a natural disaster and is buried in debt trying to avoid shutting down entirely.