Under Mason's direction, Genom Boomers recover the remains of Cynthia from the sunken wreckage of Aqua City. Meanwhile, at a Genom laboratory, the development of an upgraded Boomer is interrupted by an explosion that claims the lives of the scientists involved. At the scene, a young Chinese woman named Irene stands silently screaming. She is the fiancée of one of the dead scientists, and an aerobics girlfriend of Linna. Irene swears to expose Genom's involvement in the tragedy, Linna fears for her safety, and a mysterious group beautiful female assassin Boomers stalk them both.

Meanwhile, Priss and Leon deduce the existence of a conspiracy at Genom.

Moving from the Chinatown of Yokohama to the large Kawasaki Industrial Complex, a battle unfolds in the dead of the night, pitting Sylia's Knight Sabers against Mason's female assassin androids. Can the Knight Sabers disrupt the upgraded Boomer's development before it is too late?

From Megalocity Tokyo to Yokohama Chinatown, and finally to the Kawasaki Industrial Zone, Sylia, Priss, Nene and a much more active Linna (who had little to do in BGC 1: Tinsel City) pursue the chain of events that inexorably lead them to another confrontation with Genom.

Everyone's favorite Superconglomerate has continued towards its goal of World economic domination. The upgraded "SuperBoomer" is a weapon of great power. Using components salvaged from Cynthia, it can synchronize with the U.S.S.D. orbiting laser satellites. As they launch themselves into battle, the Knight Sabers dimly begin to see the outlines of the gigantic Genom conspiracy.

In Part 3, Genom sets it's sights on the "Urban Renewal" of Megalocity Tokyo, an endeavor that involves the use of Military Combat Boomers. The Knight Sabers are forced to confront Genom directly, and Sylia at last faces Mason in a fight to the death atop the Genom Summit.