"Neo Konchū Seiki Caucasus" is a manga series set in a dystopian future where humanity faces extinction due to environmental collapse and the rise of genetically engineered insectoid creatures known as "Caucasus." These creatures, created as a last-ditch effort to restore ecological balance, have evolved beyond human control, dominating the planet and forcing surviving humans into isolated, fortified cities. The story centers on a young protagonist, Kaito, who becomes entangled in a conflict between humans and the Caucasus after discovering a mysterious connection to the creatures.

Kaito, an ordinary teenager living in one of the last human cities, stumbles upon a dormant Caucasus queen during a routine scavenging mission. This encounter awakens latent abilities within him, granting him the power to communicate with and control certain Caucasus. This discovery draws the attention of both human factions and rogue Caucasus, each with their own agendas. The human military, led by the enigmatic Commander Akira, seeks to exploit Kaito's abilities to reclaim the planet, while a group of sentient Caucasus, led by the intelligent and empathetic Zera, views him as a potential bridge between species.

As Kaito navigates this complex web of alliances and betrayals, he uncovers the truth behind the Caucasus' creation and the role of a shadowy organization known as the Gaia Foundation, which orchestrated the ecological collapse to advance its vision of a new world order. The narrative explores themes of coexistence, the consequences of genetic manipulation, and the ethical dilemmas of survival in a world where humanity is no longer the dominant species.

The series features a diverse cast, including Kaito's childhood friend, Yuna, who becomes a key figure in the resistance against the Gaia Foundation, and Ryu, a rogue soldier with a personal vendetta against the Caucasus. The story is driven by intense action sequences, moral ambiguity, and the evolving relationships between humans and Caucasus, culminating in a climactic struggle to determine the fate of both species.