22 years ago, a bizarre uprising occurred in Japan's Yokohama region, destroying civilization, killing many, and causing the area to break off from Japan's mainland. This region came to be known as the "Lost Ground". Over the years, some of the citizens managed to erect a new city in a corner of the Lost Ground and surrounded it with a barrier to protect it from the impoverished inhabitants of the island's surrounding wasteland. However, another phenomenon began to show up in the Lost Ground: Alter, the ability to rearrange matter at the atomic level in certain ways. "Inners" who were born with Alter powers became known as Alter Users, and Alter Users who lived outside the city and misused their powers were branded "Natives". The police force known as HOLD was constructed to control Native Alter Users. A division of it called HOLY was later created and made up almost entirely of law-abiding Alter Users. Now, however, HOLD and HOLY's control over the Lost Ground has become increasingly oppressive to the point that it has started to enslave the wasteland's people. Enter Kazuma, a reckless and hotheaded Native who lives with a little girl named Kanami. Kazuma barely manages to survive off working on a farm and doing tasks for his friend Kimishima. Soon, however, Kazuma becomes caught in the conflict with HOLY and forms a fierce rivalry with Ryuhou, one of its highest officers. What is the true intent of HOLY and its leader, Martin Zigmar?