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.

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.

As the attack on Dejima escalates, the Major catches up with Kuze. She explains the whole situation to him and he agrees to follow her. They are about to leave when both are attacked by the Self-Defense forces and in the confusion are trapped under the rubble.

Togusa rescues the Prime Minister and brings her back to her office. There, Aramaki hopes her influence will stop the launching of the ultimate weapon. Meanwhile, Batou reasons with Section 4.