In the future, the Japanese government captures a class of ninth-grade students and forces them to kill each other under the revolutionary "Battle Royale" act.

A girl called Zero stands in a crowded street, her occupation an assassin. As she completes her tasks one after another, Zero has been feeling uneasy lately. As her code name suggests, she has nothing to prove her existence. She overlaps herself with the vanishing landscape and begins to wander in search of the meaning of her own existence. At the same time, a young man named One is also wandering the streets, and like Zero, he is an assassin. Surrounded by a sense of emptiness, he is unable to find the value of his own existence. One day, the two of them meet as if they were led together. They sense each other, and by touching each other, they regain their existence and humanity. However, the organization feels that contact between assassins is dangerous, and decides to dispose of them. They call in a highly skilled assassin. Their battle for their own existence begins now!

Odaiba, on the Tokyo Bay waterfront. The Odaiba Boys—a gang based here, comprising Sancon, Shu, Zaza, Jiji, Muzzle and the rest—were hanging out as usual. One day, a woman named Rei appeared before them, claiming she was searching for their leader, Nao, who had gone missing two years earlier. Around the same time, a masked man calling himself Nao appeared before rival gangs—the Kawasaki Security Squad and the Tsurumi Cruise CATS—and ran riot. Was this really Nao’s doing? Behind the scenes, a grand scheme was unfolding, orchestrated by a Member of the House of Representatives seeking to line his pockets and the Kōryū-kai, the yakuza organisation that controls Odaiba.

Odaiba, on the Tokyo Bay waterfront. Now a major Tokyo tourist attraction, lined with a giant Ferris wheel, broadcasting stations and massive shopping centres. In Odaiba, a series of disappearances involving young women had been occurring. Meanwhile, just as the Odaiba Boys’ Gang—who had grown complacent following a lull in turf wars between rival gangs—were becoming a little too complacent, news arrived that Riku of the Kisarazu Mad Dogs had been released from prison. Revenge against Nao! And he’s brought along the Tsuchigumo siblings—the ultimate reinforcements. Around the same time, the series of women’s disappearances began to take a sudden turn. Lurking behind the scenes was the smouldering scent of a turf war between the Horigome-gumi and the Tanabe-gumi. And what is the true identity of Nao, the woman who holds the key to the disappearances!? Then one day, Riku, the Tsuchigumo Siblings and the others encountered Shu, Zaza, Jiji and Mazuru…

Three junior high school students hear a rumor about the science lab and sneak into the classroom at night...