At a press conference, the Superintendent-General makes himself a prime target for the Laughing Man's threat. Section 9 has gathered enough evidence to arrest Nanao=A, but before they can, he is able to release a modular, delayed-action virus. The virus seems to only affect those on the security detail that is guarding Superintendent-General Daidō. However, Section 9 will not know who on the security team has been taken over by the virus until the symptoms begin to manifest. By that time, it may be too late.

A high-level hacking has occured at the Ministry of Health, Labour and Welfare. Section 9 has traced the source of the hack job back to a vocational aid center located high in the mountains.

The hack was done by someone very skilled since it only took two hours to crack the MHLW's ultra-secure barriers. The odd thing is that the MHLW has not filed a formal complaint about the incident. Togusa is sent undercover to discover what is going on at the aid center.

Aramaki and Kusanagi attend an international security conference in London. While there, Aramaki visits an old acquaintance of his, who is the operator of a wine fund, a place where people store their wines in order to let the wine age and become more expensive.

Their meeting is not purely a social one, but before Aramaki and his friend can sit down and talk about the old days, the bank is broken into by two mafia men.

During a visit to the Dejima Refugee Residential District off the coast of Nagasaki, Prime Minister Kayabuki receives a bouquet of flowers that is accompanied by an envelope stamped with the diamond seal seen in "NATURAL ENEMY". The envelope contains a letter that promises an attempt to take the Prime Minister's life.

At a meeting of the Prime Minister's Cabinet, Aramaki is shown the letter and told that so far the stamp on the envelope has turned up in eight other terrorist incidents. The Cabinet calls for Section 9's assistance. However, much to the unit members' chagrin, Section 9 will not be deployed in an offensive role.

During a scheduled maintenance, the Tachikomas begin to chat away about the Individual Eleven.

While talking in their new "forum", Batou and Togusa appear and take one of the Tachikomas - who just happens to be Batou's pet - with them to Spring-8 to look at the scientific evidence gathered on the Individual Eleven.

Despite close scrutiny by the authorities, the Dejima refugees declare their independence. Kuze is suspected to be the mastermind behind this new resistance and Section 9 is sent to detain him.

The Major hacks into the refugee cyberbrain hub and easily locates Kuze. When the team rushes to capture him, however, they find themselves in the middle of a trap.