Watch Ghost In The Shell: Stand Alone Complex

With all the evidence they need, Aramaki and a healthy Togusa head over to the Prime Minister's residence with enough proof to bring down the man who has pulled the strings from the shadows: Secretary-General Kaoru Yakushima. However, before they can even leave the building, the Home Affairs Minister tells Aramaki that Section 9 is suspected of being the group behind the kidnapping of Ernest Serano. Those in high places, once again, conspire to move against Section 9.

Bureau Chief Niimi has committed cyberbrain suicide, leaving Section 9 once again with no credible lead. Aramaki now decides to work on the last link to the Laughing Man Incident: Ernest Serano, CEO of Serano Genomics and the man who was kidnapped by the Laughing Man six years ago. During the past six years, Serano has continued to run his company under the protection of the Niihama Metropolitan Police. Aramaki makes an appointment to meet with Serano, but, before the interview can take place, Serano is once again kidnapped by the Laughing Man.

The arrest of the NARC Squad members allows Section 9 to move in to arrest MHLW Bureau Chief Niimi. With Imakurusu dead, Niimi is the lead that Section 9 needs to crack the case. However, several well-trained NARC Squad members still remain to be dealt with. While Motoko goes to the hospital to be fitted with a new prosthetic body, Aramaki is presented with some very troubling news.

Togusa had been shot in the chest by the DEA's Narcotic Suppression Squad, but managed to send a distress call, which is answered. At the hospital, just before he is put under sedation to be operated on, the memories in his cyberbrain are retrieved so the rest of Section 9 can view the events that led up to Togusa's encounter with the NARC Squad. Upon learning what Togusa uncovered, Section 9 moves to find Hisashi Imakurusu, who has pertinent information about a massive cover-up. Time is of the essence as the NARC Squad is also on the trail of Imakurusu.

Back on the trail of the Laughing Man, Togusa uses his investigative skills to bridge the gap between what Section 9 knows and what they don't know. After his recent failure to find the culprit of the hack job perpetrated at the Ministry of Health, Labour, and Welfare ("PORTRAITZ"), Togusa is more determined than ever to bring all the facts to light. Using J.D. Salinger's The Catcher in the Rye to help with clues given by the Laughing Man, Togusa stumbles upon an event that took place several years before the infamous Laughing Man Incident. Digging further, he comes across information vital to the case.

Over the course of several days, a large number of girls have been kidnapped. All indications point to the Northern Territories Mafia. Employing a trick known as Blindfold Ivan, the mafia is able to kidnap the girls in broad daylight with no one witnessing the abduction. Unfortunately for the mafia, they have kidnapped the daughter of the former Prime Minister of Japan, who has always publicly denied the existence of the Northern Territories Mafia. Feeling betrayed, he requests help from the Home Affairs Minister, who calls in Section 9 to assist.

A Chinese dignitary has arrived in Kagoshima, a city on the southern tip of Japan, to attend a memorial service for Chinese war dead interred there. Protesters have staked out the area, and are making sure that their voices will be heard. At the behest of the Chinese Public Security representative, Aramaki mobilizes his team to provide security for the dignitary. Covering all the angles, they come to learn that an attempt on the dignitary's life is imminent.

After attending a Security Conference in London with the Major, Aramaki goes to a bank to visit an old friend who had emigrated to England to manage a wine fund. While he visits with his friend, he allows the Major a bit of free time to walk the streets of London. Before they catch up on old times, Aramaki's friend relates to him her suspicions of possible illegal activity within the bank. As she voices her concerns, two mafia hit men prepare to break into the bank.

The Tachikomas have been returned to the lab for further study. Unfortunately for Batou, he will have little time to think about the loss of his pet. While away at a Security Conference in London with the Major, Chief Aramaki sends Batou orders to investigate one Pavlo Zaitsev. A Russian-born former boxing champ, and someone that Batou has looked up to, Zaitsev has been suspected of spying on Japan while working as a trainer for the Japanese Self-Defence Army.

Saitou tests out a new sniping device during a field exercise. Unfortunately, the device fails to make the grade. After the exercise is completed, the members of Section 9 hold a briefing session to discuss the device's usefulness. During the briefing, the Tachikomas take a look at the sniping device themselves. Finding that the problem with the device lies with its Artificial Intelligence, the Tachikomas hold their own briefing session. Worried about the Major's feelings towards them, the Tachikomas wonder if they have become too smart for their own good.

Alerted to the threat of a robbery on a financial institution by a South China mafia group, Section 9 stakes out the group's hideout in a Chinese restaurant. Posing as garbage collectors, the Major and her team move in to arrest the group before they make good on their plans.

The Japanese Coast Guard photographs Eka Tokura, a girl that had gone missing sixteen years ago, with the New World Brigade as they kept tabs on the anti-cyberisation group. Eka had volunteered to become cyberised to promote her father's technology. Shortly after, the New World Brigade kidnapped her. However, the recent pictures of Eka show a girl who looks exactly like Eka did on the day she was kidnapped sixteen years ago.

In the storage hangar at Section 9, Batou's Tachikoma starts up on its own. The Tachikoma realises that the natural oil that Batou had been giving it has altered its program since all the other Tachikomas only received synthetic oil. Opening the hangar's bay door, it takes a journey into New Port City. There, it encounters a girl named Miki who is looking for her dog. Unbeknownst to the Tachikoma, someone is watching its actions from the roofs of the city.

Several female bodies have been discovered with their torso skin cut off in the form of a t-shirt. The suspected murderer is a former American sailor named Marco Amoretti. Section 9 learned the suspect's name through the American Empire's CIA. While they investigate the case, Section 9 must allow two CIA agents to take part in the hunt for Marco.

Motoko's friend Kurutan, who works as a nurse in a hospital, asks her to help her sort out a tricky situation. One of Kurutan's charges is a little girl, who needed a new heart. The girl, Moe, was fortunate enough to receive a new heart from a donor instead of a mechanical one. For the little girl and her parents, it all seemed to good to be true. Unfortunately, it is too good to be true.

The Ministry of Foreign Affairs asks Section 9 to help them with a strange case. Marcelo Jiarti, a South American revolutionary leader, has had several attempts made on his life by such units as the U.S. Delta Force and the British SAS. However, he has survived each of these assassination attempts. For reasons unknown, Jiarti regularly visits Japan about once every five months for a total of twelve times in the past five years. The Ministry has requested that Section 9 surveil Jiarti and discover why the revolutionary enters the country so often.

With the recent death threat on the Superintendent-General's life that had been aired during a press conference about the illegal use of intercepters, Section 9 steps up their own investigation into the Laughing Man Incident. Aramaki briefs his team on a man named Nanao=A who has for some time been at the center of the investigation by the Laughing Man Unit at police headquarters. The Chief assigns Batou and Togusa to keep tabs on the man while he has the rest of the team dig deeper into Nanao's background to see if he is really the Laughing Man.

A former colleague of Togusa contacts him to ask for help with a case he has been working on. Unfortunately, before his colleague can meet with Togusa, his car plunges off of a road and explodes. Togusa is suspicious of the death because his colleague had been part of the special unit at police headquarters assigned to the Laughing Man investigation. Since it is a high profile case, Togusa is sure that his colleague's death was no accident.

Several androids have recently been employing various methods of self-termination. Coincidentally, all the androids are of the same model: The Genesis Andross GA_07JL or Jeri. Since a similar incident has occurred at the National Assembly Building with an android translator, Section 9 has been called in to assess the threat. The Major and Aramaki begin their investigation, with the help of a Tachikoma, by visiting the plant where the Jeris were produced.

The female android servants at a geisha house have gone out of control, taking as their hostages the Minister of Foreign Affairs, the Minister's secretary, the head of the Minister's Support Association, and three members of a North American business alliance. The situation is complicated by a feud over authority between the police and the military. Section 9 Chief Aramaki lends a helping hand and brings in his unit to resolve the crisis.