Set in the near future when major advances have been made in brain cyberization and cyborg technology, it delves into the hitherto unknown origins of Public Security Section 9, which combats violent criminals. Featuring a brand new cast and crew, and a screenplay by author Ubukata Tow.

While on leave, army cyborg Kusanagi receives word from her colleague Batou of a terrorist bomb threat. She rushes to the scene, but becomes suspicious upon discovering the mark of a deceased revolutionary on the chest of the ringleader.