The entire city of Nagasaki is evacuated and the JSDF moves in after a live nuclear bomb is found planted in the city, presumably by Dejima militants. Section 9 arrives to defuse the bomb and determine its precise origins.
Kenbishi Heavy Industries has built a state-of-the-art multiped tank. There's only one problem--it's gone haywire and started moving on its own. Section 9 is called in to stop it, as the Self Defense Force will not get involved. Now, it's up to Motoko, Batou, and the rest of Section 9 to stop the tank and figure out what made it go berserk in the first place.
Across Japan, a number of old JRL type Androids (called "Jeris") are destroying themselves. Section 9 is called in to investigate this mass "robot suicide" because of a potential link to another, more dangerous case. The clues lead them to a jealous owner who may have taken his Jeri too much to heart, but what is his ultimate plan?
While working late, Togusa gets a call from one of his colleagues from his days on the police force. It seems that he's uncovered something strange happening with the investigators in the Laughing Man Unit, a special task force formed to catch the infamous cyber criminal known only as the Laughing Man. But before he can meet with Togusa, he's killed in a car accident. Now, Togusa only has an envelope full of seemingly random photos to go on--can he put the pieces of the puzzle together?
The Laughing Man, having returned after a six-year absence, threatens to assassinate the Superintendent-General of the police. Everyone is in an uproar over his return. Aramaki, however, thinks it's a cover-up. He briefs Section 9 on the prime suspect, Nanao=A, an incredibly gifted programmer who developed the micro-machines that are currently the foundation of Serano Industries. Still, it's just too perfect. The team splits up and investigates.
As Togusa and Bato track down Nanao, Motoko and Paz are attempting to protect the Superintendent-General at a press conference about the police misuse of interceptors. When the virus does hit, Motoko and Paz have to act fast to save the intended victim. Meanwhile, the road to Nanao=A hits a dead end.
After being shot, Togusa's in the hospital and about to go into surgery, but he is desperate to pass on what he's learned to the rest of Section 9. As Togusa fights for his life, the rest of Section 9 takes over the case, but others within the government have learned of the investigation and are not happy. A special forces unit is dispatched to intercept them with a state-of-the-art Armed Suit.
Motoko is about to be fitted for her new prosthetic body. But when the doctor arrives and begins the procedure, it's clear that she has no intent of letting Motoko out alive. With Motoko's friend Courtin waiting outside and unaware of what's going on, Motoko must fight for her life. Meanwhile, Aramaki receives a disturbing message that his brother has been kidnapped.
The Laughing Man returns! And, just as he did six years ago, he kidnaps the president of Serano Genomics without being detected. Section 9 arrives at Serano's house too late, and sets out to find him. The Laughing Man and Mr. Serano discuss what happened six years ago, and why Mr. Serano hasn't fulfilled his promise. This time, however, things are going to be different, with or without Serano's help.
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