On her first visit to one of the refugee areas, the Prime Minister receives a bouquet of flowers with a death threat in it. Section 9 is called in to provide round-the-clock security for her as they work to catch the would-be assassin. As they do their legwork, more and more links to the mysterious "Individual Eleven" are uncovered.

Meanwhile, Togusa is trying to unravel the reason for a man's suspicious death, and it leads him into the bowels of Tokyo and a government cover-up. Then, Section 9 is ordered to transport some dangerous plutonium out of one of the refugee districts, and the creepy Gohda is once again given command of the operation.

When it's all over, the Major and the rest of Section 9 try to figure out exactly how all of these things are linked together. These strange happenings can't all be coincidence.