Acting on a tip, Section 9 breaks up a cabal of thieves hell-bent on wrecking a Japanese financial institution. Shortly after the raid a Chinese intelligence official contacts Section 9 and informs them of suspicious activity that he believes may indicate an assassination attempt by Chinese Socialists on a prominent, yet reclusive, Japanese multi-millionaire.

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.

A botched arms deal reveals that the government's plans to remove Plutonium from the Shinjuku dig site ("EXCAVATION") by sea have been compromised. Section 9 is called in to take the Plutonium out of Old Tōkyō by land.

The members of Section 9 are not happy being used by the government. Batou is especially incensed since Section 9 is supposed to be an offensive organization. His patience will be further tried when he and Section 9 find out who will be accompanying them on their mission...

Section 9 has uncovered Shō Kawashima's ("FAKE FOOD") external memory device on the net. Hidden in a route to the Asian matrix only accessible through the European array, Section 9 concludes that the device was hidden by Gouda. Unfortunately, Gouda has left no trace of his movements in the device.

The Major prepares to dive into the device with Bōma and Ishikawa watching her closely. However, before she can dive, Aramaki notifies her that someone even more important than the external memory device has just surfaced...

Ishikawa returns from the Peninsula with the latest intel on Kuze, but is surprised to learn of a possible refugee uprising. The Major and Aramaki are sent to see the Prime Minister to discuss this matter and the existence of "hub cyberbrains". While they wait, the rest of the team listens to Ishikawa's report on Kuze's past.