Synopsis

At night, Major (ret'd) Motoko Kusanagi crouches high on top of a harbour crane and monitors the police radio.At the airport, Togusa arrives in his Infiniti SUV to lead a group of Section 9 agents to storm a hostage situation. A Colonel Ka Gael has taken a female hostage. Surrounded by Section 9, Ka Gael is high on drugs and says fearfully that "the Puppeteer", is coming before shooting himself in the head. An eavesdropping Kusanagi takes note and drops into the night.Aramaki walks to a waiting VTOL with a young aide, Proto. He talks to Prime Minister Kayabuki about a recent string of suicides by the followers of General Ka Rum of the Seok Republic, including the man's eldest son Ka Gael moments ago. The PM won't allow Section 9 to interrogate The General, who is under house arrest, for political reasons. Aramaki decides to disobey her and leads a raid on Ka Rum's home.Batou is at another police crime scene, another Seok suicide victim and follower of General Ka Rum. Aramaki sends Batou to investigate another lead.The Section 9 team in the VTOL discuss the political reasons for the PM's decision, Japan was somehow forced to allow General Ka Rum asylum and there are six other countries involved. The General had vowed to lead a reign of terrorism if his country Seok fell, which it did.Landing at a secure island, Section 9 enters the buildings in optical camoflage. They find the General dead, seemingly having killed himself. Ishikawa notes the dead man had been linked to the a medical 'net using it to contact his operatives. They discover plans for Seok operatives to deploy a micromachine virus in a terrorist attack but are puzzled by the suicides. Ishikawa says there is a program running to make it look like the General is still alive, it appears the death was an asassination disguised as a suicide. Before he died, Ka Rum wrote "Puppeteer" on the floor in his own blood. A webcam records the scene and the Section 9 discussion, they decide not to report the dead body.Batou and a Hatchikoma are going to intercept a man named Ma Shaba, the operative who received the micromachine virus, he sees a lone car parked outside the hospital location. Just ahead of him Kusanagi is also going to Ma Shaba. She takes a large box from a refrigerated cabinet. Suddenly a large six-legged walking tank attacks the Major, Batou sees her from a distance. Ma Shaba is in hysterics driving the armoured vehicle. The Hatchikoma is damaged. Batou and the Major chat briefly. The Major leaps on top of the tank and unlocks the hatch. The man inside is dead. The Major takes the box and warns Batou to stay away from the Solid State Society before driving away in Batou's Ford GT.Batou does not reveal to Section 9 that he encountered the Major, claiming instead that Ma Shaba attacked him, for no apparent reason. Section 9 develop a theory that the Puppeteer is a hacker surpassing "wizard class" who hacked into the Seok agents' cyberbrains and forced them to commit suicide.Inside the hospital Togusa discovers sixteen kidnapped children. The team think that Ka Rum's revenge plot was to disseminate the micromachine virus into the public using the children as carriers.The Major enters a room and enters a glassed-in pod, another male figure exits another pod and leaves with the box from the hospital. In a large room the Major sits at the controls of a large machine fronted by a huge display screen. As she gets up to leave an android falls to the ground and the Major tells herself "controlling two remote bodies is my limit".Back at Section 9 HQ Saito arrives from a tough assignment in Africa. Togusa leads a team brainstorm session, there is a missing terrorist named Raj Puhto out of the original Seok group of 16. 144 ampules of the micro machine virus are missing. Togusa thinks a third party was present at the hospital battle with Batou, the person may be the Puppeteer although Batou denies seeing anyone else.Section 9 observes the recovered 16 children. They determine their cyberbrains had the memories partially erased and their personal IDs assigned to fake parents. In each case, the fake parents were "Noble Rot Senior Citizens", bedridden elderly connected to the health care nursing network, which takes care of their basic needs but results in its users becoming nearly comatose. Section 9 is puzzled on why the children had been kidnapped by the Seoks. Togusa orders further digging into the records.At the Ministry of Heatlth, Labour and Welfare Batou's yellow car enters the parking lot.Section 9 discovers a discrepancy in the records of various government agencies that suggests that over 20,000 unreported child kidnappings had taken place over the last two years. Suddenly their computer is infected by a Class E virus, Batou has to use a fire axe on the power cables to stop the hack. Aramaki arrives with the box of Seok virus ampules, they had been left at the MHLW Pathogenic Microorganism Isolation Facility. Aramaki suggests the Puppeteer is a government agent and to let the whole matter rest, other than identifying the 16 children. Aramaki goes to his car, Batou is waiting in the backseat waiting to have a private conversation with the Chief. Aramaki admits he made a deal with the Prime Minister, and the government Treaty Review Department had General Ka Rum killed. The two men also discuss the future of Section 9, Aramaki says Togusa is being groomed for the leadership.There is an emergency in Room 47, Section 9 agent Proto is ready to shoot himself and the rescued children are missing.Aramaki goes to visit a bedridden and senile Colonel Tonoda, attended by scantily-clad maid-bots. Also there is Aramaki's old friend from Intelligence who gives him a file.Batou tells Togusa about his encounter with the Major, and his suspicion that the Major may be the Puppeteer.Aramaki orders Batou to take Saito and search for Raj Puhto, a Seok operative and elite sniper who was the commander of Ka Rum's personal guard, recently seen in