Kusanagi is with new Section 9 recruits as an examiner, when she suddenly finds herself into an unfamiliar place. She meets two child cyborgs and an old woman. The woman promises Kusanagi that she will tell her about the cyborgs the next time Kusanagi visits her. The Section members are suspicious of Kusanagi's disappearance during the recruiting exam. After returning to the real world, at first she avoids the other members, and eventually decides to goes back to hear what the old woman has to say.

Kuze escapes from the Kyushu Tower. Section 9 starts another investigation pursuing the fact that only few specialists could have actually created Kuze's unique prosthetic face. They rush to the face craftsman who might be the primary witness, but find him murdered. The face of the murderer in the security video is exactly that of Paz. The man is perplexed, but soon remembers this might be connected with an incident he was involved in years before. What ever happened in Kuze's past?