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 Japan. They locate him in a taxi on a highway and tail him in circles around and around a tall double office tower complex. Meanwhile, Togusa tracks one of the sixteen children to the apartment of a Noble Rot Senior Citizen connected to the health monitoring system.In the Treaty Review Department Archive Room a man greets a buxom blond version of Major Kusanagi calling her the Puppeteer. She refunds a payment then goes blank, the body was a puppet.Togusa finds one of the missing kids sleeping in an old man's decrepit apartment. The man was named as the boy's guardian in the boy's altered personal ID. When Togusa picks the boy up, the man arouses from his comatose state to demand the return of the child, saying that he has named the child as his sole heir as he would rather leave his assets to a stranger rather than to the government, and claiming that the child would have been abused if he were not placed in his care. He says that this is the will of the Solid State, and warns that if Togusa interferes with their enterprise he will become another suicide. The man dies immediately afterward. Togusa gives the boy over to the Children's Aid, pointing out the ID error. Afterward, he comes to the realization that had he not interfered the boy would have been passed on to social services and adopted after the death of his Noble Rot Senior Citizen guardian. This, he realizes, was the plan of the Solid State all along as other senior citizens stare at him. Togusa receives a phone call from his wife saying that his daughter has gone missing. He rushes home.The taxi finally stops and lets Puhto out, he turns on his invisibility optical camoflage and the two Section 9 lose track. Saito guesses where he may be, Batou spots the man from afar as the Seok sniper aims at a man riding in a limo. Saito wounds Puhto with a long range shot. Batou then questions Puhto who reveals that he had received intelligence from a man named Munei that identified his target as the mastermind of the assassination of Ka Rum. However, it is quickly discovered that Munei himself was Puhto's target. Batou suggests that Puhto may have been set up by the Puppeteer. Puhto agrees that this may have been the case, and says he would kill the Puppeteer if it were human. He claims that the Puppeteer is a mechanism built into the Solid State, which he identifies as the health care monitoring network, and implies that the Japanese government is stealing children.When Togusa reaches home it turns out to be a false alarm, as his daughter was only at the neighbors'. He decides to drive her to school. While driving Batou calls to recap and express his hunch that the Seoks somehow found out about the nursing net and planned to use if for their own purposes. Then Togusa takes a call on his daughter's cell from a disguised voice that starts to hack him, and he is made to drive to a cyberbrain hospital. He is also tracked down by Batou and Section 9, who realized that he had been hacked. During the hacking, Togusa converses with a voice he believes is the Puppeteer. He realizes that this was how all of the children were abducted: the parents' cyberbrains were hacked, and the parents were made to personally escort their children for a cyberbrain transplant operation. Afterward, the parents' memories were altered to make them forget they ever had the child. Togusa accepts that he has to kill himself to save his daughter and brings his gun up to his head. Batou is running but is too far to reach him. As Togusa starts to squeeze the trigger the Major materializes and stops him just in time, Batou comforts the scared little girl.The Major explains that she stumbled across the case of the missing children while wandering alone through the net in the years since she left Section 9, and set up Togusa as bait to unmask the identity of the Puppeteer. She explains that the Puppeteer is a gestalt running on a hub cyberbrain, Batou links to Motoko to get the whole story. Three virtual tachikoma AIs, assist her in locating the current location of the hub cyberbrain: the Sacred Citizen Relief Centre, the double office tower where the health care monitoring system is managed.The Major rejoins Section 9 to help the investigation. They focus on Hitoshi Munei, a reactionary conservative member of the House of Representatives who advocates a racially pure Japanese ruling class, he has links to the Treaty Review Department. The Major explains that she had a contract with the TRD to carry out Ka Rum's assassination. However, by the time she got there, the Puppeteer had already killed Ka Rum. Munei also wields control over the Sacred Citizen Relief Center, which he and other politicians arranged as a front for an "elite training facility" - a brainwashing factory to develop new members of the elite. The Major speculates that Munei was targeted for elimination by the Puppeteer because his brainwashing facility was interfering with the goals of the Solid State Society, which housed kidnapped children at the same facility.After analyzing the building's systems and layout, Ishikawa determines that the Centre was designed and built with the kidnapping setup included from the beginning, which means that the Puppeteer must have been involved from the start. Section 9 decides to raid the Centre with the help of the Major's Tachikomas, who are returned to new physical bodies. Kusanagi and Togusa split up as they fight large bipedal security cyborgs and armed androids. The Major finds a main computer terminal and starts to hack in.Inside, Chief Aramaki confronts Munei in a room where many children are wearing large helmet headsets. The Assemblyman admits to taking money from the Noble Rot Senior Citizen project to fund his "education" program. He justifies it by arguing his program is for the future of Japan. Togusa reports there are only 3000 kids on site . Munei says he was unaware of the Solid State abduction system, believing the children in his program were orphans. A man, Tateaki Koshiki, steps forward and claims responsibility for the Solid State system. He shoots himself in the head. The Major plugs into the dying cyberbrain before his memories are lost as Batou uses a Tachikima to provide a power boost.Motoko links with the brain and she goes limp. Koshiki explains that his actions were motivated by several problems: The more than six million Noble Rot Senior Citizens, the rising unemployment rate and shrinking working population, the low birth rate, and the fact that over 50 thousand children die needlessly each year as a result of abuse. The Solid State Society was his attempt to recycle the ghosts of the Noble Rot Senior Citizens and help the abused children. He altered the household registrations of children in high-risk homes to place them in the care of the Noble Rot Senior Citizen, giving the children new opportunities and giving the Noble Rot Senior Citizen a purpose in life, as well as the ability to leave a successor despite their lack of children, and to prevent their estate from being seized by the state upon their death. The Noble Rot Senior Citizens readily agreed to participate. Koshiki further elaborates that he attempted to eliminate Munei because he wanted to brainwash the children to become part of the elite cadre, which was counter to the goals of the Solid State Society, which wanted the children to have free will.Koshiki then reveals his trap. He shot himself in the head so he could hack into the Major'smind and eliminate Section 9. With control over the Major's cyberbrain, he makes her see his face as images of Batou, Togusa, the Laughing Man, Kazundo Gouda, Chief Aramaki, Hideo Kuze, and finally the Major herself. A flashback to an earlier scene showed Koshiki as the puppet leaving the Major's spare body nest .The Major passes out as Koshiki's cyberbrain dies in a whiteout. She stirs lying facedown in an electronic cot.Aramaki and Togusa discuss the future of the abducted children, who will be returned to their parents. Aramaki says they just have to follow the rules and not judge.Batou explains the story of the real Koshiki to the Major when she regains consciousness. Tateaki Koshiki, age 33, was a fast track civil servant who grew bored with no sense of purpose. Due to his high cyberbrain skills he had been recruited by Munei but he programmed his own abduction system into Munei's. He gained special permission to work entirely from home but no one noticed when he died two years ago because he never personally dealt with anyone. In this time, his cybernetic body continued to act under the Puppeteer's or the senior citizens gestalt control. Batou says that the Tachikoma may have kept a record of the Major's conversation with Koshiki but the tank claims that it was erased in the white out when he died. Batou may have his own memory of the conversation although he says it all doesn't really matter now does it?The Major relfects on her recent past andlooks out on the city, and says "The net is truly vast and infinite."