The story is set in a distant future where Japan is divided into feudal territories and conquered by other countries. There is a floating city named Musashi that is composed of eight ships in the skies. A war that will determine the fate of the world will be fought by students on the Musashi.

In the far future, humans abandon the devastated Earth and ascend to the upper world "Tenjo", taking on new, god-like form. But even with their newfound "Godhood", humanity eventually fell into war, resulting in the collapse of Tenjo and the very law of causation, and humanity, having lost their divine powers, returns to the Earth, grown largely uninhabitable, with the exception of a portion of the Far-East (modern-day Japan), which they name "Shinshuu" (Divine States"). As Shinshuu alone is too small to accommodate all of humanity, they duplicate the region in a parallel world they called "Juusou Sekai" (Harmonic Realm"), calling their new territories "Juusou Shinshuu" (Harmonic Divine States). In order to rebuild Tenjo and the law of causation, the returned humans start a reenactment of history, starting from 10,000 BC, following the guidance of historical records from a source known as the "Testament". In the year 1413 TE (Testament Era), the reenactment of the Nanboku-cho War in Shinshuu inadvertently damages the mechanisms separating the worlds, causing Juusou Sekai to collapse into the original world. The humans living in the Juusou Shinshuu thus lost their land, and decide to invade the original world. The people of Shinshuu are defeated, and under the terms of their surrender, their territory is divided by the invaders, and discriminatory laws are imposed on them. Reenactment of history is resumed from 1457AD, but the updates to the Testament unexpectedly end at 1648 AD. A rumor of impending apocalypse begins to spread the world.