The Lost Ones are wanderers who come here from a distant world known as "Japan." No one knows how or why they leave their homes. The only thing that is certain is that they bring disaster and calamity. The duty of exterminating them without remorse falls to Menou, a young Executioner. When she meets Akari, it seems like just another job...until she discovers it's impossible to kill this girl! And when Menou begins to search for a way to defeat this immortality, Akari is more than happy to tag along! So begins a journey that will change Menou forever...

At the beginning of chaos, the world was divided into three realms: the realm of deities, the realm of men, and the realm of demons. The realm of deities sent a spirit seed down into the world to help the common people. But the spirit seed continuously absorbed the evil of the world and cruelly harmed living things. In the end, Sen Luo, the king of the deities, sacrificed himself and sealed it. However, because of it, the Shangqing Xianmen, where the realm of deities is located, gradually waned and was lost in history. A thousand years later, the ruins of Shangqing Xianmen started to appear in succession. All major sects fought their hardest for possession of the treasures in the ruins.

Deep in the Ararat Mountains of Turkey, a secret organization known as ARCAM has found what is believed to be Noah's Ark. However, the U.S. Machine Corps., a rogue organization of the Pentagon, wants to take over the Ark as a means of global supremacy. Only a special ARCAM operative known as a Spriggan stands in their way. Japanese Spriggan Yu Ominae teams up with French Spriggan Jean-Jacques Mondo to combat members of the U.S. Machine Corps. led by Col. MacDougall—a genetically-enhanced boy with deadly psionic powers. However, they must act fast and stop MacDougall before he uses the Ark for his own agenda.

Shu is from Datania, a country that makes young children work. He and his friends were trying to escape when they met the Returners. The Returners are some kind of rebels to Datania. Shu goes with the Returners to fight Zero, Nines, and his men who are after DT, a special substance inside humans.