Long before the era of prehistoric man, an advanced alien species inhabited Earth. Negligent of the power they held, these beings ultimately caused their own demise. However, the aliens left behind a warning to future civilizations on indestructible tablets: to destroy any remains of the ruinous technology created by their kind. In modern times, the ARCAM Corporation and their paramilitary unit—the Spriggans—seek to seal the relics away and prevent renegade actors from exploiting their powers. Following ARCAM's recent discovery in the Ararat Mountains of what is believed to be the mythic Noah's Ark, Spriggan Yuu Ominae has been dispatched to investigate. However, the site is ambushed by the US Machine Corps—a radical faction of the Department of Defense led by Colonel MacDougall. On the Pentagon's orders, MacDougall seeks to secure ARCAM's lead scientist and seize the artifact. Teamed up with fellow Spriggan Jean Jacquemondo, Yuu must stop MacDougall and the Machine Corps' elite soldiers from advancing on the Ark before it is too late. Arcam is a secret, worldwide organization investigating artefacts from a lost civilization. When three of their investigators go to Mt. Ararat, in Turkey, they discover what they believe is the wreck of Noah's Ark. Their joy is short-lived, and so are they — the relic projects a powerful, destructive energy which wipes out not only the team but three Pentagon satellites as well. Quickly, Arcam and the US military are battling for the Ark's secret. Arcam's trump card is their super-powered warrior agents, called Spriggans. One Spriggan, a high school student named Yu Ominae is dragged into the fray. He makes his way to Turkey to confront the Pentagon's platoons. Of course, the Americans have super-soldiers of their own, including the human tank Fat-Man and the vicious Little Boy. The bullets are soon flying en masse, in what has become a holy war for the future of the human species.