Much time has past since the end of the refugee issue and Section 9 has changed with it. Now a larger force, Section 9's only handicap is it is without the skills of Major Motoko Kusanagi, who left over two years ago. Togusa is now in charge of the section that will be put to the test when a mysterious entity dubbed the Puppeteer emerges and begins killing off members of a disenfranchised group of ex-military.