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Centered around a young girl, Genocyber details the creation of the ultimate biological weapon, created out of two psychic sisters. Starting off in Hong Kong, the story follows a young mute girl who is unwittingly dragged into the ambitions of a mad scientist who wants to combine the powers of the girl and her crippled sister to activate the Genocyber itself. After a brutal search that leaves dozens of corpses in its wake, the search ends when the girl is apparently captured by agents of a shadowy government organization and the scientist arrested. This proves to be wrong however and the girl escapes, killing the scientist and government agents in the process.

A country called Karain has withdrawn from the United Nations in protest of the new World government and launched an invasion of a neighboring country.

The Vajra attempts to fuse itself with Genocyber but Genocyber's psychic powers prove to be stronger and the Vajra loses control of its body and the consumed carrier, which detonates in a massive explosion.

Genocyber is on a rampage of destruction. It is revealed that for 100 years, humanity has been waging a desperate and hopeless war against Genocyber, which has decimated the Earth.

Genocyber then attacks the city, killing the mayor and all its citizens. Soldiers attempt to stop Genocyber, but their weapons prove useless, and they too are killed and when the rampage is over, the entire city has been left in ruins.