Many years after the events of Last Bible II, humanity and beasts have settled into uneasy coexistence. In the game's prologue, the war hero Alek Messena collapses at the gates of the underworld, whispering hope that his old friend Glen Larsford survived.
The story begins with Glen's son Ciel, who lives an ordinary life—studying the supernatural energy known as gaia at school—while vague references to the devastating Polisian War, ended fifteen years ago, linger in conversation. When soldiers attack Ciel's village and target his father, Ciel is forced to unravel the connection between Glen, the fallen Polisian States, and the Phelesteau perpetual engine—a machine that powers entire cities in exchange for its citizens' promise never to release gaia within city limits.