Basically there's a secret society of extremely powerful bad guys led by a mysterious grandmaster who's trying to acquire and unlock ancient technology said to have been left behind by the Goddess.
Rean Schwarzer is a freshman in a Military Academy who's placed into a special, extra-curricular class put together by the prince of the Empire, a reoccurring character across previous games, in a hope to create the strong people he needs to reform the Empire into something better in the future (The prince doesn't tell the characters this, of course).
Rean and his new classmates are thus given extracurricular activities which include exploring an ancient ruin left behind centuries ago disguised as an old school house behind the school, as well as being sent to various places across the Empire to resolve issues and give Rean and his classmates first-hand experience of the political and social issues that plague the Empire.
As the plot unfolds, the ruins below the school house turn out to be something so much more significant than just ruins, and also during these field trips across the Empire, Rean and his class are unintentionally slowly dragged into a terrorist conspiracy that's just a front to start something so much larger, a civil war between a Noble faction and Reformist faction, which is also just a front for the aforementioned secret society mentioned at the beginning of the post to try and reach their goal using the chaos.
Basically there's a giant mecha at the bottom of the ruins in the old school house. Your school senior is the secretly the leader of the terrorist group that started a civil war between Nobles and Reformists. There's a secret society playing both sides in the background to get their own way.