After years of beating Black Ghost all the 00 Cyborgs have moved ob with their lives going to their home country to pursue a career they wanted to do. Dr. Gilmore and 001 have been living at the laboratory in the years of peace, although Dr. Gilmore's research assistant Dr. Cosmo has been striving to find the existence of a super energy source out in space that he's named "The Vortex" and seeks to gain control of. But for Dr. Gilmore, all he would prefer is a peaceful retirement. Once this force is seen as a threat Dr. Gilmore has no choice but to call back the 00 Cyborgs to fight once again.

Motoko Kusanagi and the rest of Section 9 encounter Takashi Shimamura, leader of the refugee group N. A post-human raid begins in the ruins of Tokyo, where the evolutionary singularity is fast approaching.