Continuing their journey from Record Country (the place that held the book of memories), Syaoran and company land into Tokyo Country, a blood-filled country under war from opposing factions for natural resources and survival. While reluctantly involved in the race to live, the group faces their own problems as certain revelations are made, changing their journey forever. A shocking betrayal and a battle that risks all of their lives. After this revelation, they will never be the same again.

U.C. 0097, one year after the opening of "Laplace's Box." Despite the revelation of the Universal Century Charter that acknowledges the existence and rights of Newtypes, the framework of the world has not been greatly altered. The conflict later dubbed the "Laplace Incident" is thought to have ended with the downfall of the Neo Zeon remnants known as the Sleeves. In its final battle, two full psycho-frame mobile suits displayed power beyond human understanding. The white unicorn and the black lion were sealed away to remove this danger from people's consciousness, and they should now be completely forgotten. However, the RX-0 Unicorn Gundam 03, which disappeared two years earlier, is now about to show itself in the Earth Sphere once more. A golden phoenix... named Phenex.

Someone out there is determined to see the fall of Weiss Kreuz, and it looks like they have found the perfect plan for it. The four assassins find themselves trapped in a deadly game of deceit, where the question of honor versus duty comes to surface. Now they must fight for their own reasons to survive--and there can be only be one victor in this field of death.

Aya, Yoji, Ken, and Omi are the four young men who comprise Weiss Kruez (WK), an assassin group who eliminates certain menaces to society. Each member has his own trademark fighting style. Aya is adept at fighting with a katana, Yoji has mastered the art of strangulation via strings, Ken is lethal with his metal claws, while Omi specializes in a wide array of projectiles. Under the command of a mysterious man known only as "Persia", the WK is dispatched to take care of drug rings, terrorist factions, and the like. But as things go along, they discover that most, if not all, the bad elements they have dealt with are somehow connected to the Takatori family. The Takatori family is rich, powerful, and influential. It seems if the problem is to be nipped in the bud, the WK would have to put an end to one of Japan's most prominent clans.