The story focuses on Class Zero, a group of fourteen students from the Vermillion Peristylium, a magical academy in the Dominion of Rubrum. When the Militesi Empire launches an assault on the other Crystal States of Orience, seeking to control their respective crystals, Class Zero is mobilized for the defense of Rubrum. Eventually, the group becomes entangled in the secrets behind both the war and the reason for their existence. The setting and presentation were inspired by historical documentaries, and the story itself was written to be darker than other "Final Fantasy" titles.