Protesters start gathering in Niihama, calling for the government of Japan to return stolen water to war orphans. Major Motoko Kusanagi, a contractor for Public Security, stands above a building watching the protests. She claims that "it's starting" as all lifelines, surveillance systems, door locks and other electronically controlled systems are dominated by Section 9. Chief of Public Security Daisuke Aramaki leads his AI intelligence team to analyze the 4022 people isolated in that area. He hears complaints from other departments in Public Security but dismisses them as he tracks down a recently mobilized Qhardi group. Vice-Minister Kitahara contacts Aramaki and he fills her in on the details, to which he specifies the Yotsubashi building as the terrorist's target. The Major's team meets for a cyber-briefing, discussing the possible involvement of a high profile hacker named "Fire-Starter". With the help of police, Borma and Paz catch a potential Qhardi agitator in the crowd but note the suspicious lack of weaponry. Suddenly, the police officers overseeing the protest open fire on the crowd, killing multiple civilians and then each other. Ishikawa calls this the biggest Ghost-hack ever, but the Major remarks that there is no tech that allows the control of that many people. She surmises that instead of a hack, this attack was likely a virus. Leaving the cyber-meeting the Major jumps off the roof of the building and activates her optical camoflauge. Meanwhile a member of security in the ball room that Kitahara was attending is affected by the virus and shoots her, with the speaker still continuing her speech. The Major appears behind the speaker, Dr. Zhinzhee Bekka Arr Thied, and shoots her with optical camo on covering her identity. She makes her escape running towards the window and leaping out of it. Her audio line is hacked in midair by a female voice telling her that she can't stop Fire-Starter. A helicopter appears and shoots at the Major pushing her body back into the building. Batou calls for Saito to retaliate. Saito activates his infrared vision and snipes the pilot, sending the chopper flying. The Major is okay and runs into the hall, discovering a Logicoma already stationed with optical camo. They defeat another insurgent and escape the building. Back at the scene of the protest every civilian is dead except for a single young girl. Batou and Togusa appear and hold her up but notice that a sniper's crosshair is pointed at her. Batou tackles her to the ground as the Major shows up and is also targeted. She calls for Saito to take the other sniper down but he doesn't catch him in time. The next day the Major is lectured by Aramaki for executing Dr. Thied but she claims that he has no proof. Aramaki doesn't buy her story and questions her ability. Kusanagi then asks for details of the suspect and Aramaki profiles her as Emma Tsuda, a famous game app maker. When the Major says the information isn't enough, Aramaki urges her to join Section 9 for greater oversight and benefits. Suddenly, Colonel Hozumi of army intelligence enters the room and demands "ex-Major" Kusanagi to be taken into captivity on suspicion of Ghost infiltration. Kusanagi corrects her claiming that her intel is outdated and that her rank as Major had been reinstated. Aramaki tells Hozumi that the government does not acknowledge Ghost infiltration as possible, and that Kusanagi has already been transferred from Unit 501 which puts her under his direct authority. Hozumi promises Aramaki that he'll regret this and leaves. With Hozumi's claims in mind, Aramaki approves of Kusanagi's assassination the previous night and assigns the Major's team to the job of escorting Tsuda to Unit 501 for analysis. The team of Kusanagi, Togusa and Batou get in a van and prepare for Unit 501's dissection of Emma Tsuda.