In a distant past before humanity, ancient aliens inhabited Earth but faced their downfall due to their own careless actions. Leaving behind unbreakable tablets as a cautionary message, warning against the dangerous remnants of their advanced technology, they vanished. Fast forward to the present day, where the ARCAM Corporation and their elite force, the Spriggans, dedicate themselves to safeguarding these ancient relics from falling into the wrong hands. When a possible artifact linked to the legendary Noah's Ark surfaces in the Ararat Mountains, Spriggan Yuu Ominae is assigned to investigate. However, their mission is jeopardized by the US Machine Corps, a radical faction aiming to seize the discovery under Colonel MacDougall's command. Amidst the chaos, Yuu teams up with fellow Spriggan Jean Jacquemondo to thwart MacDougall's plans and prevent the Ark from being exploited by the enemy forces.