A prototype multiped tank has destroyed two other prototypes and broken out of a testing facility. Section 9, employing its own smaller multiped, the Tachikomas, is brought in to stop it.

The hijacker is using the ID of the tank's designer who had recently died. Whoever is operating the tank, their motives are unknown. Section 9 has little time to figure out these two mysteries before the tank enters the urban area.

A certain type of android, the GA07_JL, nicknamed Jeri by its users, has been affected by a virus. Recently, all Jeri model androids have been committing "suicide".

Section 9 is called in as it may be related to a virus detected in an android at the National Assembly Building.

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.

While tracking the New World Brigade, an anti-cyberization group, to an unused radiation scrubber facility off Okinawa, the Japanese Maritime Safety Agency took pictures that show Eka Tokura, the kidnapped daughter of a cyber-technology company CEO. However, the girl had been abducted over 16 years ago when she had been 10 years old. In the recent photos, she looks just as she did on the day she was taken.

For reasons unknown, contact with the Maritime Safety Agency's reconnaissance team has been lost. Section 9 heads to the facility to locate the unit and find out why Eka Tokura was there.

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.

Several bombings have occurred throughout New Port City. Each time, Section 9 arrives too late to stop their detonations. With a fifth and final bomb set to go off somewhere in the city, the unit puts all of the information they have found from the first four bombings together.

Even the Cabinet Intelligence Service is having their fair share of difficulties. A hacker has infiltrated its incredibly advanced computer security system. The hacker enters the vast array of information stored at the CIS and begins to collect data...

Training has commenced to find new recruits for Section 9. With Motoko acting as the target, Batou and Togusa watch as the recruits try to keep up with the Major.

After ditching some of the recruits, Motoko has to lose just one more pair. She ascends some stairs in an alley and the recruits follow her. Moving out into the street above, the recruits see that they have lost the target. However, Batou and Togusa have lost contact with the Major as well.