"Ghost in the Shell S.A.C. Solid State Society 3D" is a feature-length anime film set in the same universe as the "Ghost in the Shell: Stand Alone Complex" series. The story takes place in 2034, two years after the events of the second season, and follows Section 9, a covert counter-cyberterrorism unit, as they investigate a series of complex and interconnected cases. The narrative centers on a mysterious entity known as the "Puppeteer," who manipulates individuals through cybernetic implants, leading to a string of suicides and kidnappings. The Puppeteer’s actions are tied to a larger conspiracy involving the exploitation of the elderly and the manipulation of societal systems.

Major Motoko Kusanagi, the former leader of Section 9, has left the unit under unclear circumstances, leaving Togusa as the acting chief. Togusa struggles to balance his leadership role with the demands of his personal life, particularly his responsibilities as a father. As Section 9 delves deeper into the Puppeteer’s activities, they uncover a plot involving the "Solid State Society," a shadowy organization that uses advanced technology to control and exploit vulnerable populations. The investigation reveals that the Puppeteer’s ultimate goal is to create a utopian society by erasing the memories and identities of those deemed unfit, effectively rewriting their "ghosts" or souls.

The film explores themes of identity, autonomy, and the ethical implications of technological advancement. Key characters include Batou, who remains a steadfast member of Section 9 and serves as a bridge between the team and Kusanagi; Togusa, whose human perspective contrasts with the cyberized members of the unit; and Kusanagi herself, who reappears in a mysterious capacity, raising questions about her motives and connection to the Puppeteer. The narrative intertwines personal struggles with broader societal issues, culminating in a confrontation that challenges the boundaries of human consciousness and the role of technology in shaping society. The film maintains the philosophical depth and intricate storytelling characteristic of the "Ghost in the Shell" franchise, while advancing the ongoing narrative of Section 9 and its members.