The Major and Batou are flown to Berlin in an effort to track down a terrorist called "Angel's Feathers". While there, Batou attracts the attention of a young girl in a wheelchair.

Much to the chagrin of Batou, Motoko, and the rest of the team, Kuze and the refugees manage to escape in one of the camouflaged boats. They are further hampered when an explosion causes heavy losses, leaving them unable to follow the fleeing boat.

The city of Fukuoka is evacuated when a live nuclear bomb is found. With the Dejima Refugees targeted as the prime suspects, the government sends the Self-Defense Forces into the city.