Major Motoko Kusanagi, a cyborg, leads Section 9, a clandestine unit that battles terrorism and cyber warfare; she confronts The Laughing Man, a terrorist who has resurfaced from the past; Motoko and her team try to unmask his identity.
Togusa is released from jail and learns about the dissolution of Section 9; out of work and depressed, he tries to find information on the others, but there is nothing available; with nothing left to lose, he goes to assassinate the man responsible.
The Laughing Man returns and kidnaps the president of Serrano Genomics without being detected; Section 9 arrives at Serrano's house too late and sets out to find him.
Events begin to shift into overdrive; while things seem to be going Section 9's way, people in the shadows are starting to appear; Motoko arrives at the hospital to switch to a new prosthetic body; Togusa begins the recovery process.
After being shot, Togusa's in the hospital and about to go into surgery, but he is desperate to pass on what he's learned to the rest of Section 9; as Togusa fights for his life, the rest of Section 9 takes over the case.
Superintendent-General Daidō has been publicly threatened by the Laughing Man; through an intermediary, the Laughing Man demands that Daidō reveal the truth or else he would be removed; Section 9 continues their own investigation into the incident.
A certain type of android, nicknamed Jeri by its users, gets affected by a virus; all Jeri model androids are committing suicide; Section 9 is called in as it may be related to a virus detected in an android at the National Assembly Building.
After going on a destructive spree at the testing facility, the tank heads towards the urban area of Niihama; Section 9 is called in to stop the tank, as no terrorist group has claimed responsibility, and the JSDF refuses to involve itself.
Public Security Section 9 is an elite special operations unit; they've been called in to rescue a high-ranking government official from a hostage situation; something doesn't seem right to Major Motoko Kusanagi.
