"Biomega" is a science fiction manga set in a dystopian future where humanity faces extinction due to a deadly virus known as the N5S. The virus transforms infected individuals into grotesque, zombie-like creatures called Drones. The narrative centers on Zoichi Kanoe, an agent of the Toa Heavy Industry, who is tasked with locating Eon Green, a young girl believed to hold the key to curing the virus. Zoichi operates with advanced technology, including a powerful motorcycle and a sentient AI companion, Fuyu Kanoe, embedded in his neural system.

The story unfolds across a sprawling, decaying urban landscape, where Zoichi encounters various factions vying for control over the remnants of civilization. Among these are the Public Health Service, a militarized organization attempting to contain the outbreak, and the Data Research Foundation, a shadowy group with its own agenda. As Zoichi pursues Eon Green, he uncovers deeper layers of conspiracy involving artificial intelligence, human experimentation, and the origins of the N5S virus.

Key characters include Nishu Mizunoe, a Data Research Foundation agent with a personal vendetta against Zoichi, and Kozlov Grebnev, a former scientist whose experiments with the virus have catastrophic consequences. The narrative is marked by intense action sequences, intricate world-building, and a focus on the ethical implications of technological advancement and biological manipulation.

As the story progresses, Zoichi's mission becomes increasingly complex, revealing connections between the virus, the AI systems controlling society, and the fate of humanity itself. The manga explores themes of identity, survival, and the blurred line between human and machine, culminating in a climactic confrontation that challenges the very nature of existence in a world dominated by decay and transformation.