Set in the mid-21st-century, the manga tell the story of the fictional counter-cyberterrorist organization Public Security Section 9, led by protagonist Major Motoko Kusanagi.

The manga contain Shirow's thoughts on design and philosophy, including sociological issues, the consequences of technological advances and themes on the nature of consciousness and identity.

Starting in 2019, a collaborative manga by Junichi Fujisaku (writer) and Yuki Yoshimoto (illustrator), titled Ghost in the Shell: The Human Algorithm, was made as the sequel to GiTS 1.5.

The level of cyberization varies from simple minimal interfaces to almost complete replacement of the brain with cybernetic parts, in cases of severe trauma.

The heroine of Ghost in the Shell, Major Motoko Kusanagi, is such a cyborg, having had a terrible accident befall her as a child that ultimately required that she use a full-body prosthesis to house her cyberbrain.

As the investigation continues, Section 9 discovers that the Puppet Master is actually an advanced artificial intelligence created by a department of the Japanese government, taking up residence in a robot body.

Ghost in the Shell 2: Man-Machine Interface[e] This story is set four years and five months after Motoko Kusanagi fused with a sentient life form and left Public Security Section 9.

As she delved into the investigation, she found herself making contact with other isotopes when infiltrating Motoko Kusanagi in a secretive club known as the "Sleeping Universe," a facility used for the transfer of consciousness.

[4] Kōichi Yuri, First Coordinator at Young Magazine, requested a "more flashy" name and Shirow came up with Kōkaku Kidōtai (攻殻機動隊, Shell Squad).

[7][better source needed] Shirow's thoughts and work on Ghost in the Shell contain numerous footnotes and detailed explanations about scenes to give readers an understanding of the sociological differences or technological advances and philosophical discussion of the material.

Cyborgs are shown consuming food, but Shirow noted that early in the development would have been pills or paste substance that would have both psychological and physical functions.

[8] Other personal beliefs of Shirow are represented in the scenes and author's commentary, such metaphysics, religious references, and other philosophical stances that enter a range of topics including his thoughts on a rotating universe.

Toren Smith commented on Studio Proteus's actions claiming that requirement of the "mature readers only" would translate into a 40% loss in sales and likely have caused the immediate cancellation of the series.

[9] The sequel volume Ghost in the Shell 2: Man-Machine Interface also featured explicit scenes and an increase in nudity in the "Short-cut" version in Japan.

[10][better source needed] Ghost in the Shell ran in the Kodansha's manga anthology Young Magazine Kaizokuban from the April 1989 to the November 1990 issues,[11][12][13] and was released in tankōbon format on October 2, 1991.

The box set also contained a booklet titled ManMachine Interface Inactive Module, a poster, and a Fuchikoma robot action figure.

A VR Noh stage play adaptation was presented in Tokyo's Setagaya Public Theatre on August 22 and 23, 2020,[48] and has since also been performed in Fukuoka and Sapporo.

Meanwhile, a television series release began in 2002 under the title Ghost in the Shell: Stand Alone Complex, telling an alternate story from the manga and first film, featuring Section 9's investigations of government corruption in the Laughing Man and Individual Eleven incidents.

Publishers Weekly praised the manga for its artwork: "Masamune's b&w drawings are dynamic and beautifully gestural; he vividly renders the awesome urban landscape of a futuristic, supertechnological Japan.

"[53] Leroy Douresseaux of the website ComicBookBin gave the manga an "A" stating: "It is visually potent and often inscrutable, but its sense of wonder and exploration makes its ideas still seem fresh two decades after its debut.

"[54] Peter Gutiérrez of the website Graphic Novel Reporter praised the manga, writing: "In short, Ghost in the Shell is hard sci-fi of the best possible sort: the type that's so full of both undiluted artfulness and philosophy that it's arguably a must-read even for those who don't usually take to the genre.

"[55] Greg McElhatton of Read About Comics praised the artwork, however criticized the manga for its story pacing and collection of short adventures stating, "I'm glad I got to experience Shirow's artistic view of the future and am a little interested in the idea of his Intron Depot art books, but on the whole Ghost in the Shell was a massive shell game: flashy and fascinating from a glance, but ultimately empty when you decide to dive in.

"[59] Publishers Weekly praised the artwork as "the color and b&w graphics are stunning, brilliantly evoking the nonvisual world of data transmission" but stated that the story can be confusing.