Tomoro Tenma lives in a world where human thoughts and emotions, known as e-Pulse, power AI devices called Sapotama. But when Digimon begin materializing from Sapotama and feeding on e-Pulse, society begins to fracture.

In 2045, cybernetic mercenary Motoko Kusanagi returns to Section 9 to face dangerous threats.

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.