Motoko enters into an online chat room devoted to the Laughing Man to see if she can find any new information on him. What she discovers is a spirited debate among the self-proclaimed "fans" of the Laughing Man, but very little hard evidence.
Togusa is on the trail of the Laughing Man again, and this time, his investigations lead him towards both a leading micromachine corporation and an NGO called the Sunflower Society. As he visits with one of the officers of the Sunflower Society, however, the building is attacked by especially well-armed troops!
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.
The government orders Section 9 disbanded. Aramaki is taken away, and Togusa is arrested. Motoko assembles the remaining team members at HQ for one final mission. They prepare for a full-scale assault while Elite troopers and Armed Suits descend on Section 9 HQ.
The Major heads to Taiwan to investigate a lead on Kuze, and ends up getting involved with local gangs and a troublesome kid.
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