"Scryed" is set in a post-apocalyptic Japan, where a mysterious phenomenon known as the Great Uprising has caused a portion of the land to rise into the sky, forming a new region called the Lost Ground. This area becomes a lawless zone where society's outcasts and criminals reside. In this world, certain individuals, known as Altered, develop supernatural abilities called Alter powers, which manifest uniquely for each user. These powers are often tied to their personalities or desires, granting them extraordinary capabilities.

The narrative centers on Kazuma, a rebellious and independent Altered who lives in the Lost Ground. Kazuma possesses the ability to transform his right arm into a powerful, energy-based weapon. He operates as a vigilante, taking on jobs to help the downtrodden while clashing with the authorities. His life takes a dramatic turn when he encounters Ryuho, a member of HOLY, an organization tasked with maintaining order and controlling Altered individuals. Ryuho wields the power to manipulate gravity, making him a formidable opponent. Despite their opposing roles, Kazuma and Ryuho share a complex rivalry that evolves throughout the story, driven by their conflicting ideals and mutual respect.

As the plot unfolds, the conflict between the Altered and HOLY intensifies. HOLY seeks to suppress and exploit Altered individuals, viewing them as threats to societal stability. Kazuma and Ryuho are drawn into a larger conspiracy involving the origins of the Great Uprising and the true nature of Alter powers. Their paths cross with other key characters, such as Kanami, a young girl with a mysterious connection to the Lost Ground, and Cougar, a ruthless Altered with ambitions of domination. The story explores themes of power, freedom, and the struggle for identity in a fractured world.

The narrative builds toward a climactic confrontation between Kazuma and Ryuho, as their personal ideologies and the fate of the Lost Ground hang in the balance. The resolution of their conflict ties into the broader mysteries of the world, revealing the consequences of humanity's actions and the potential for redemption. "Scryed" combines action, drama, and science fiction elements, delivering a story that balances intense battles with character-driven moments. The series is notable for its exploration of moral ambiguity and the complexities of its protagonists, making it a compelling entry in the genre.