"Blue Seed Beyond" is a sequel to the original "Blue Seed" series, continuing the story in a post-apocalyptic setting where humanity faces new threats from ancient, malevolent forces. The narrative centers on Momiji Fujimiya, a descendant of the Kushinada lineage, who possesses the unique ability to combat the Aragami, monstrous entities that threaten the world. Alongside her is Kusanagi, a member of the Terrestrial Administration Center (TAC), an organization dedicated to protecting humanity from supernatural threats.

The plot unfolds as Momiji and Kusanagi investigate a resurgence of Aragami activity, which is linked to a mysterious artifact known as the "Blue Seed." This artifact holds immense power and is sought after by both humans and Aragami, leading to a series of intense confrontations. The story delves into the origins of the Aragami, revealing their connection to ancient Japanese mythology and the gods. As the conflict escalates, Momiji must confront her own heritage and the responsibilities that come with her powers.

Key characters include Momiji Fujimiya, whose growth and resilience are central to the narrative; Kusanagi, whose loyalty and combat skills make him a crucial ally; and various members of TAC, each contributing to the fight against the Aragami in their own way. The series also introduces new antagonists, including powerful Aragami leaders and human conspirators who seek to exploit the Blue Seed for their own gain.

Themes of sacrifice, duty, and the clash between ancient traditions and modern technology are explored throughout the series. The narrative maintains a balance between action-packed sequences and moments of character development, providing a cohesive and engaging storyline. The resolution of the series ties together the various plot threads, offering a conclusion that addresses the immediate threats while leaving room for potential future developments.