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.

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.

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.

=A hacker and thief by the name of Cash Eye plans on infiltrating a vault during a party, and Section 9 is called in to prevent it. But there are a number of strange elements in this case that don't all add up.

An assassination threat has been made against Prime Minister Kayabuki; Section 9 is called to serve as bodyguards Meanwhile, investigation on the Individual Eleven turns up some interesting history.

While on a stakeout of a Taiwanese vegetarian restaurant, Section 9 finds out that someone is pulling strings and feeding misinformation to the Public Safety Sections.

Following a tip, the Major conducts an undercover investigation of Kuze in Taiwan. While there, she saves a boy running from the Mafia.

The government declares martial Law in Dejima, believing that the refugees have a nuclear device and plan to use it to gain independence. When the refugees' connection to Kuze is cut off, one shot begins a bloody war.

The tables seem to be turning in favor of Section 9, but the nuclear missile is still being prepared for launch.