The Minister of Foreign Affairs behaves strange after a hostage situation in a restaurant. Section 9 is sent to investigate.

A battle tank is on the loose. Section 9 must investigate who is behind all this. The tachikoma's are deployed to stop the tank.

Jeri-type androids are committing suicide massively. A virus seems to be the cause of this. Section 9 must seek the responsible person.

A police detective makes discoveries on the Lauching Man. He is assassinated before he can publish his findings. Section 9 investigates the matter.

After six years of absence, the Laughing Man strikes again. This time he threatens the police head commissioner.

Section 9 is still looking for the Laughing Man, who appears in various shapes. Meanwhile, the police head commissioner must be protected.

Section 9 keeps an eye on the famous revolutionary Marcello Jarti, who is suspiciously visiting Japan on a regular basis.

A young girl discovers her newly transplanted heart may have come from a less-than-legitimate source, spurring Kusanagi to undertake a personal crusade.

Kusanagi eavesdrops on a futuristic chat room dedicated to the crimes committed by the Laughing Man, only to discover several of the chat room participants aren't what they seem to be.

Batou must come to terms with a dark chapter from his own past when he is called upon to track down a brutal serial killer.

Togusa is sent to investigate a mysterious government facility for the treatment of 'cyberbrain closed shell syndrome.' What he encounters may hold the key to the Laughing Man mystery.

One of the Tachikoma is acting strange after being out all day with a little girl. The contents of the cyber brain that the Tachikoma found, alarms Section 9.

A girl that was kidnapped 16 years ago, suddenly appears in public again. Meanwhile, a sophisticated boats gets lost. Does the girl, one of the first cybernized people ever, have something to do with it?

Criminals have information about a rich banker. Because it is suspected that an assassin is sent, Section 9 takes on the protection of the banker.

The Tachikoma are questioning themselves about life and death. Section 9 is displeased by their behavior, which is becoming more individualistic.

Batou is on a mission to investigate a former boxing champion, who is suspected of espionage.

Aramaki goes to visit an old friend in London, who suspects a secret book-keeping in the company she works for. Their meeting takes an unexpected turn.

The Chinese Minister of Foreign Affairs is threatened during a visit to Japan. The main suspect is the son of an old, deceased friend of Aramaki.

The daughter of the former prime minister is abducted by a terrorist group that he has always denied existence of.

Togusa makes new discoveries on the Laughing Man. He investigates the matter.

Section 9 is seeking for the fugitive doctor Imakurusu, however, they are not the only one.

Major Kusanagi gets into trouble when she is transferred into a new host body. Aramaki investigates the abduction of his brother.

The director of Serano Genomics is abducted again. Things get clearer on his first abduction, years ago.

Section 9 is compromised, and the authorities seeks ways of dismantling the Section.

With Batou and Motoko the only remaining members of Section 9, Batou undertakes a risky sortie to Motoko's apartment to recover her hidden weapons cache.

The final episode completes the first stand alone series. Togusa is released from prison but has no idea what has happened to section 9 members and still can not believe that the chief abandoned them. Episode reveals what happened to the members of section 9 and has a long conversation with the laughing man that wraps up the series.