In a post-apocalyptic world, a mysterious event known as the "Great Uprising" has reshaped the landscape of Japan, creating a wasteland called the Lost Ground. Within this region, certain individuals, known as "Alter Users," possess unique supernatural abilities called "Alters," which manifest as powerful extensions of their will. These abilities vary widely, ranging from physical transformations to energy manipulation. The series centers on the conflict between two factions: the Native Alter Users, who live freely and often use their powers for personal gain, and HOLY, a government-sanctioned organization tasked with regulating and controlling Alter Users to maintain order.

The protagonist, Kazuma, is a hot-headed and independent Native Alter User with the ability to generate a powerful exoskeleton-like armor around his right arm. His life takes a dramatic turn when he encounters Ryuho, a disciplined and stoic officer of HOLY, whose Alter allows him to summon a massive, dragon-like energy construct. The two initially clash due to their opposing ideologies: Kazuma values freedom and self-determination, while Ryuho believes in strict order and the greater good. Their rivalry intensifies as they repeatedly confront each other, each driven by their own motivations and principles.

As the story progresses, deeper layers of the Lost Ground's history and the origins of Alters are revealed. It becomes apparent that the Great Uprising was not a natural disaster but the result of human experimentation, and the Alters themselves are tied to a mysterious energy source known as the "Original Alter." Both Kazuma and Ryuho are drawn into a larger conflict involving HOLY's true intentions, the enigmatic scientist Dr. Kanzaki, and the potential for a second Great Uprising that could destroy the world.

The narrative explores themes of power, freedom, and the consequences of human ambition. Kazuma's journey evolves from a self-centered pursuit of strength to a deeper understanding of responsibility and the impact of his actions on others. Ryuho, meanwhile, grapples with his loyalty to HOLY and the moral ambiguity of their methods. Supporting characters, such as the compassionate Kanami and the enigmatic Cougar, add depth to the story, each contributing to the exploration of the series' central conflicts.

The series builds toward a climactic confrontation between Kazuma and Ryuho, as their personal rivalry becomes intertwined with the fate of the Lost Ground. The resolution of their conflict reflects the broader struggle between chaos and order, individuality and conformity, leaving lasting implications for the world and its inhabitants.