The entire premise of "Arifureta" is built on a series of escalating revelations. The first major twist is the identity of Hajime's betrayer: his classmate Daisuke Hiyama, who acted out of jealousy. However, the true mastermind behind the class's suffering is another classmate, Eri Nakamura, who is a necromancer in league with the demons and the god Ehit, driven by a psychotic obsession with the hero, Kouki Amanogawa.
The central conspiracy of the world is that the god who summoned the heroes, Ehit, is a malevolent, insane being who treats the perpetual war between humans and demons as his personal game. The 'heroes' are merely his pawns, meant to be disposable entertainment. The Great Labyrinths were not created as trials for heroes, but as rebel strongholds by a group of ancient magic users known as the Liberators, who failed to overthrow Ehit in the past. Hajime's quest to conquer the labyrinths is, unknowingly at first, a journey to inherit the Liberators' will and their unique 'Ancient Magic'—the only powers capable of killing a god.
In the final arc of the story, Ehit possesses the body of Yue, seeking to use her immense power as his new vessel. Hajime and his party must travel to the Holy Precincts, a divine realm, to confront Ehit directly. The final battle involves not only Hajime's party but also his reconciled classmates and the armies of both humans and demons, who unite against their common divine foe. Hajime, using all the Ancient Magic he has acquired, manages to defeat Ehit. The series concludes with Hajime and his entire party successfully using their combined power to create a gate that allows them, along with all his classmates, to return to Earth, bringing their adventures in Tortus to a definitive end.