The third season of .

Seven years ago, Chu Yunfei was struck by a dramatic change in his family and was stranded in the Pill King Valley in Zhongzhou. He returned to his homeland to take revenge and vowed to find out the truth.

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... [Written by MAL Rewrite]

In 1929, Ladd Russo spared Graham Specter's life and earned his unwavering loyalty. Three years later, Graham is infuriated upon learning that Ladd was pushed off the train after the events aboard the Flying Pussyfoot. As a man of bizarre yet passionate philosophies, he plans to make an offering to Ladd by kidnapping Eve Genoard and subsequently capturing Jacuzzi Splot, who has been living in the Genoard mansion with his gang. Meanwhile, Jacuzzi and his gang take in an unfamiliar woman, Elmer C. Albatross pays a visit to the prison to meet an old friend, and Czeslaw Meyer runs into the man he hoped he would never see again. These seemingly separate storylines merge, tying up several loose ends and revealing the whole truth of the anomaly that occurred aboard the Advena Avis in 1711. [Written by MAL Rewrite]