It has been years since the Seven Year War ended and peace finally arrived.
The story begins with the protagonist, Zero, making his living as an independent contractor.
One day he is investigating a certain site. It is there that he finds a mysterious stone infused with a powerful magic known as the Core Elemental. As he takes on more and more jobs to investigate other locations, he discovers more and more Core Elemental stones.
On his travels, he begins to encounter the Human Genomes — new creatures created by God to replace mankind. One thirsts for power. One desires only the eradication of mankind. And one hopes to retrieve what he has lost.
To get what they desire, each one appears before our protagonist. Through his battles against the Human Genomes, our protagonist begins to learn the truth about the secret of his birth, and before long finds himself at the very place where he was born.
Finally, he will learn the truth of his existence.