In the year 2410, the distant planet Tinos is a harsh world where humanity cannot survive without a chest-implanted life-support device called the Biomatrix. The Planetary Government, or Star Government, tightly controls the production and approval of these devices, using them to enforce obedience. Those who resist are branded as the Lost and are systematically exterminated, along with their children—the Lost Number Children.

Seventeen-year-old Blue is one such Lost Number child, living in the squalid Ninth District of Junk City. When he tries to obtain a Biomatrix to save a dying infant among his group, he is captured and executed by government agents. But Blue is rescued by an obsolete, spherical robot named Fats, who carries a prototype Neo Matrix—a next-generation life-support system that can adapt the human body to Tinos without external aid. Fats fuses with Blue, reviving him as a Cyber Being, a hybrid of human and machine with superhuman strength, bulletproof skin, the ability to hack into others' memories, and the potential to evolve through mutation.

Now reborn as Cyber Blue, he sets out to protect the remaining Lost Number Children and bring down the Star Government. Along the way, he is aided by Maria, a government official who secretly sympathizes with the Lost and later reveals her own hidden past as a Lost Number child herself. The government's leader, Cliff, seeks to seize the Neo Matrix for himself, unleashing a series of horrors: bio-engineered chimeras, genetically modified child soldiers like Emiliano, and elite operatives such as the cyborg soldier Jin Cykes, a former Lost who lost his loved ones in a previous rebellion and now blindly believes the government's cause is just.

Volume by volume, Blue fights through increasingly brutal encounters—against a rocket-firing mecha piloted by the effeminate Colonel Kokoro; against the super-heated bio-being ignited by the Firefly parasite; and against Jin in a climactic duel where Maria sacrifices herself to reignite Blue's Neo Matrix after it is disabled. Finally, Blue storms the government's stronghold to face Cliff, carrying the grief of the planet and the hopes of the Lost Children.

The story weaves a classic rebellion narrative with cyberpunk themes of bodily autonomy, genetic manipulation, and the dehumanizing cost of authoritarian control. Blue's journey from a hunted boy to an evolving symbol of resistance forms the emotional core, while Fats provides both comic relief and the inherited knowledge of a lost scientist named Plum, who designed the Neo Matrix to free humanity. The series concludes with Blue's final confrontation to decide the fate of Tinos and the survival of the Lost Children.