Akira Hose, Colonel Hozumi and Dr. Thied engage in a cyber meeting plotting conspiracy, where Hose pleads for the release of the Qhardi group that was arrested by the Major's team through Hozumi, in exchange for exclusive data. She agrees and assigns him an "Ariel" unit. Meanwhile, the Major is seen meeting up with Lt. Col. Kurtz who advises her to take down Scylla permanently. When she gets home, she notices that her left leg is still affected by the Fire-Starter virus. She is visited by Hose who reminisces over their first meeting. He remarks that her confusion over the blurred differences between human and machine is what interested him in her from the beginning, and they embrace. The Major's team meets briefly the next day, with Batou noting that she has high heels on. Kusanagi then leaves for a ball where she meets up with Hose for a date. They each discuss the growing changes in human society with the advent of prosthetic bodies and the Ghosts that inhabit them. They come home and lay in bed with each other, but are suddenly interrupted by a hitman who unsuccessfully tries shooting them in their sleep. Hose appears behind him and tells Kusanagi to run. She stays to help him however, and the attacker escapes. She goes to tend to him and apologizes for involving him in the dangerous operation. Later, a melancholic Major is seen sitting in the Public Security headquarters being consoled by Chief Aramaki and Batou. Batou notes that her attacker was a professional despite his failure to kill the two. After confirming Hose's safety, the Major commands her team to search diligently for any traces of Scylla, seemingly making the case personal. Detective Togusa appears and requests the Major for questioning. When he implies that she isn't thinking straight after her lover was attacked, she is angered and picks him up by the collar. Togusa tries to convince her that Akira Hose is too suspiciously connected to the case. Hose is then shown meeting with the rest of the conspirators trying to leave the group, but is forced to remain and "become Scylla" himself. The Major barges in to the room where the Qhardi leader is imprisoned and synchs through him, asking him of Hose's identity. He claims that he is the new Scylla and is responsible for giving him the virus that infected the Major to begin with. Convinced, Kusanagi and Batou meet with Togusa to ask him for aid in the operation. Togusa cites Dr. Thied as the most likely suspect for providing arms to the Qhardi group. The Major's team, led by Aramaki, meet with Vice Minister Kitahara to warn her of being a target to the terrorists. One of her men is suddenly affected by the virus and the entire facility is attacked. Hose is then seen giving his data to Kurtz of the 501, who is standing next to Emma Tsuda. He asks for info of Scylla to which she tells him that the information is available in his infected cyberbrain. The Major accepts that Hose is Scylla and tells Batou that she would take care of him. Togusa and Batou then find the warehouse that harbors the prosthetic bombs called "Ariel" but are attacked by the Major's would-be assassin. The Major is then seen holding up Hose, who begins to tell her about his connection to Scylla. However, his body is revealed to be holographic and Kusanagi spots the real Hose outside escaping with Dr. Theid. Batou continues to wrestle with the attacker and questions the Ghost hacking method used against him as the same that the Major uses. The rest of the Major's team is seen dealing with the attack on the Vice Minister's office and she tells them that her cyberbrain was packaged through her time with Hose, and created a copy of. Eventually, Major Kusanagi catches up with Akira Hose who was attempting to board a helicopter. They both raise their guns and approach each other. After multiple shots, they hold their guns at point-blank range. Hose reveals that it was his cyberbrain that was packaged and that his death would save her and her friends. He points the gun at his head instead and claims that he was glad to have met her, calling her Scylla. He shoots and kills himself. Afterwards, Batou explains that the Major was actually Scylla, and that she helped the Qhardi separtists before faking her death. She tells him that she is suffering an identity crisis, not knowing who she actually is. The Major decides to go through another prosthetic surgery to help her feel more unique. Togusa discovers that his superior officer, Mizuki, was also in on the Qhardi scandal with huge sums deposited into his account before death. He is met by Kusanagi outside who asks if he would join her team. Before she gets to finish however, he receives a call from his wife who tells him that she is going through labor with their first child. He runs off to meet her, leaving the Major bewildered.

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