In a world covered by an endless sea of sand, there sails an island known as the Mud Whale. In its interior lies an ancient town, where the majority of its inhabitants are said to be Marked, a double-edged trait that grants them supernatural abilities at the cost of an untimely death. Chakuro is the village archivist; young and curious, he spends his time documenting the discovery of newfound islands. But each one is like the rest—abandoned save for the remnants of those who lived there long ago. For the first time in six months, another island crosses the horizon, so Chakuro and his friends join the scouting group. During the expedition, they find vestiges of an archaic civilization. And inside one of its crumbling remains, Chakuro discovers a girl who will change his destiny and the world inside the Mud Whale as he knows it.

Following the closure of the Laughing Man case, Section 9 is re-established by Japan's newly elected Prime Minister, Youko Kayabuki, to combat the persistent threat of cyber-terrorism. A group calling themselves The Individual Eleven has begun committing acts of terror across Japan. While Motoko Kusanagi, Daisuke Aramaki, Batou, and the other members of Section 9 investigate this new menace, the Japanese government faces a separate crisis, as foreign refugees displaced by the Third World War seek asylum in Japan. But as the members of the special-ops team continually encounter Gouda Kazundo—a leading member of the Cabinet Intelligence Service—in their hunt, they begin to suspect that he may be involved, and that the events of the refugee crisis and The Individual Eleven may be more connected than they realize...

A powerful necromancer known as the Corpse God dies during a legendary battle, only to be reborn as Polka Shinoyama, a young boy in modern-day Tokyo. In the process of trying to adapt to his new physical body, he gets targeted by various groups that deal with the supernatural. Among them is Misaki Sakimiya, a high school girl who can see spirits and is out for his blood from the very moment they meet. Attempting to make sense of this situation where unknown parties want him dead, Polka eventually meets Takumi Kuruya, a contractor skilled in surveillance and hacking, and Lisa Kuraki, a crime boss operating out of Shinjuku. Alongside these—and other unexpected—allies, Polka braves danger to reveal the truth of his reincarnation and the fate awaiting the world he now lives in.

One day, a man claiming to be a god suddenly hacks a certain school's intercoms, ordering all of its students to team up and prepare to be transported to another world. There, they will be given special skills in the hopes that they become that world's heroes and defeat the Demon King that ravages the land. The initial transfer is a success. However, Seiichi Hiiragi, who suffers from his classmates' constant bullying due to his somewhat undesirable appearance, is left behind as no one is willing to be his teammate. Nevertheless, the self-proclaimed god decides to send Seiichi to the parallel world and lets him join his peers. Unfortunately, this fateful ordeal causes Seiichi to arrive at a location deep in the forest, far not only from his schoolmates but from human civilization as well. Desperately searching for a way to change his predicament, Seiichi's miserable days only seem to continue to worsen. Yet when all hope seems lost, Seiichi discovers a strange fruit known as the Fruit of Evolution—which may be his first step toward a significantly better future.