In the near future, humanity has reached a point where complete body replacements from organic flesh to mechanical parts are possible. This advancement greatly enhances both physical and cybernetic abilities, blurring the line between the two realms. However, criminals also take full advantage of such technology, resulting in new and often highly dangerous forms of crime. To address these innovative threats, the Japanese government establishes Section 9, an independently operating police unit that handles such sensitive criminal cases.
Led by Daisuke Aramaki and Motoko Kusanagi, Section 9 deals with these crimes across the entire social spectrum, usually achieving success. Yet, when faced with a new elite hacker nicknamed "The Laughing Man," the team is drawn into a dangerous game of cat and mouse, following the hacker's trail as it leaves its mark on Japan.