During an invasion by an alien organism called "Savage," humanity"s only defense is a weapon dubbed the "Hundred." Hayato Kisaragi, a teenage survivor of a Savage strike who exhibits the greatest compatibility with this device, is summoned to hone his abilities at Little Garden, an elite naval academy on a warship where advanced training modules and historical battle simulations are conducted daily. Throughout his rigorous preparation for the looming conflict in a world that has already been reshaped by the alien threat, he quickly attracts several female classmates and becomes entangled in numerous events as he battles the creatures that now roam Earth, jeopardizing its safety today.