Public Security Section 9

Major Motoko Kusanagi is dispatched by Section 9 to spy on a building in New Port City. A foreign power conspires to recruit a domestic programmer to fix the Project 2501 "bug." The team moves in while Major activates her thermoptic camouflage. The foreign official refuses to return the programmer, while Kusanagi moves in and kills him.

During the investigation of the Laughing Man case, Major Kusanagi poses as the Laughing Man in order to uncover a conspiracy against Serano Genomics, a nanotechnology (micro machine) company by the Japanese government. After higher-ranking government officials uncover information about the Section 9 investigation, the government disbands the agency and declares war on them.[1]

In preparation for an attack on their headquarters by the Umibozu's shock troopers and their Type 303 Armed Suit robots, all remaining Section 9 members barricade themselves into the building and fight the invaders with heavy weaponry.[1] Failing that, they assemble a diversion and escape through a passage in the sewers of New Port City. They are all eventually captured, with the Major apparently killed.

Togusa spends the next three months wondering what happened to the rest of Section 9 before encountering Batou. The whole thing turns out to have been Aramaki's plan, sacrificing Section 9 in order to leave the prime suspect wide-open to arrest, investigation, and prosecution.[8] Everyone, including the Major is fine, and Aramaki is in the process of rebuilding and securing funding for the newly-reborn Section 9, which happens in 2nd GIG.

The second season starts with Section 9 non-existent in an official capacity due to an amendment to the Special Forces Bill. The first episode involves a hostage situation in which nine terrorists, who call themselves the Individual Eleven, are holed up in the Chinese Embassy, demanding a swift change in the Refugee Action Policy. They demand the freedom of the refugees from the stand point that refugees drain the country. The previous PM of Japan issued a temporary bill that allowed for the entrance of refugees into certain zones, but the bill was never repealed. Because the new PM, Kayabuki, plans to repeal the policy soon, she has to act quickly on the terrorists before their demands become known in order to ensure it doesn't appear that she was caving in to terrorist pressure.

Section 9 is promised full reestablishment, and the approval of their new budget proposal that includes the reinstatement of think tanks (Tachikomas), on the condition that there are no hostage casualties in the process of stopping the terrorists before the press blackout runs out. From this point on the 2nd season goes on to focus on the refugee issue from multiple perspectives, along with providing additional background information on almost all of the characters.

A new group emerges in this season, The Individual Eleven. This group first appears in the premiere episode as a group of Individual Eleven "copycats" take hostages in the Chinese Embassy. Later in the series it is revealed that the Individual Eleven's true intentions were to harm the wellbeing of refugees that had taken shelter in Japan at the end of World War IV. This group destroys itself in a public display of mutually assisted suicide among the members. Only one survives, Hideo Kuze, who then sides with the refugees and confounds Section 9 as to his motives.

Section 9 is radically reformed after the Major leaves in order to pursue investigations of her own. The section has increased in size, and is now run by Togusa because Batou declined the position. Solid State Society initially focuses on the cyberbrain suicides of members of a terrorist organization that gained asylum in Japan. This case leads to the discovery that around twenty thousand children may have been abducted. The mastermind behind the crimes is known as "The Puppeteer," and is classified as a Super Wizard Class Hacker.

Arise is an alternate universe telling of the formation of Section 9. Major Kusanagi, an ex-army hacker, is recruited by Aramaki and charged with putting together a team to deal with high level hacking threats. Over the course of the series, while pursuing her own personal investigation, she encounters and works with (sometimes double crossed by) all of the original team members. At the end of the series she offers them positions on her team. A notable change is that Togusa is involved from the beginning rather than being recruited some time after the team's formation.

According to Tawanda Manyimo, part of what makes the Section 9 group so interesting is they aren't controlled by the government. "We are able to cut through red tape and bureaucracy it seems," he said "Who doesn’t want that? We can actually just do what we want, in essence. And we answer to essentially to Aramaki and the Major, so we’re almost a rogue renegade, but not quite. And I think that’s a unique position because in the world, there is a lot of political intrigue."[9]