A refugee boat escapes from Etorofu; Section 9 tries to follow from the air with their tilt-router, but the aircraft suddenly explodes just before Kusanagi and Batou's eyes. Without a vehicle, Section 9 starts a secret investigation of Sagawa Electronics, the company involved in the nuclear material transaction. They come across a dark shadow in the Information Bureau. Meanwhile, the refugee boat makes a smooth return trip until the coast guard vessels surround them just before arriving in Dejima. Could Kuze and his group return to Dejima safely through the blockade?

After the declaration of independence, the refugees are almost at their peak with anticipation. The government decides to send in the armed forces. In this turmoil, Aramaki desperately proposes a plan to the prime minister. In order to put this into action, Section 9 hijacks a helicopter and heads for Dejima. At the Dejima Bridge, the two sides are at stand still when a single gunfire pushes the situation to the worst.