Shirow Masamune's classic manga about a cyborg SWAT team and its CO in Post-Cyberpunk Japan. It would go on to become a franchise, being followed by two more manga series, GitS: Human Error Processor and GITS: Man/Machine Interface, and later being adapted into two animated films and an anime. The films and Stand Alone Complex are in different continuities. A live-action film is in Development Hell.
Alternate Continuity/Revision: When Shirow Masamune first set out to write a sequel to Ghost in the Shell, he published what would become Human Error Processor in a magazine. When it was time to give it a stand-alone, paperback release, he'd realized that he had a much greater story to write, and released Man/Machine Interface, without saying a word of what he'd done. (Shirow is notoriously secretive.) The fan-reaction was..less than stellar, and eventually Human Error Processor was released as GITS 1.5. While the two sequels can be taken as a continuous continuity from Ghost in the Shell, there are some finer details that don't quite match up.
Ascend to a Higher Plane of Existence: Maj. Motoko Kusanagi basically witnesses Project 2501 all-but-literally fulfill this trope when she dives into its dying ghost. Soon afterwards, Project 2501 returns and joins with Motoko to become a new type of lifeform. Because this is Shirow Masamune, two of these lifeforms later join forces to ascend once more by merging with an artificial silicon lifeform.
Barbie Doll Anatomy: Averted until the last quarter or so of Man/Machine Interface, when Motoko spends a lot of time diving. Shirow said in a margin note that he stopped drawing her nipples for convenience's sake.
Bi the Way: Motoko enjoys creating illegal pornographic software with her roommates, but also has a boyfriend named Sugi, in who works in Section 1.
Brain Uploading: Ghost dubbing allows someone's ghost to be copied and inserted into other bodies, such as a clone, but the result is always more limited or more insane than the biological version, and the original suffers heavy brain damage and eventually death as a result. Ghost dubbing is illegal because of the clones or other embodiments that are released as a result (along with the said death of the original). Each and every one of those clones is the original copy of the soul. Attempting this process is punishable by life in prison or having your brain wiped. Batou and Togusa come across a ghost dubbing system in one chapter while investigating sex bots gone berserk, where it turns out that the ghosts of kids smuggled into the country by the mob were being dubbed into said bots.
Butt Monkey: Batou tends to be this for Motoko quite often.
Togusa of all people, gives one in Human-Error Processor while gloating his seniority over Azuma after he pissed off a woman they were tasked with escorting safely back home.
Batou can be seen with these when he's in a good mood.
The Fuchikomas often sport these whenever they're depicted with mouths for comedy's sake.
Motoko is depicted with one in a small panel near the end of the first manga.
Even Aramaki pulls one off every now and then when he's really sticking it to a political opponent.
Chameleon Camouflage: In the various incarnations this is known as thermoptic camouflage, presumably because it also works in infrared.
Characterization Marches On: Motoko's not nearly as stoic here as in the anime adaptations. As the volumes shift from dark comedy to a more serious plot though, the Major's characterization loses the upbeat nature and becomes colder and pensive, much like later adaptations characterizes her.
The lesbian threesome in the original manga, and several shots of female service androids in revealing outfits.
Man/Machine Interface goes out of its way to provide crotch shots, and for one panel, Motoko being pleasured by cyber-tentacles.
Gainaxing: Kusanagi, who else?!
Girl on Girl Is Hot: Years after the first volume was published Shirow admitted that the only reason he drew an all girl orgy was because he "didn't want to draw some guy's butt."
Heart Drive: Cyborgs usually only have their organic brain encased in a cyberbrain shell as the last remaining organic part of their body. Very few people are shown to be able to survive without having it directly inside their body.
Hollywood Encryption: Done with the Hand Wave that the Major and the more techie members of Section 9 are just that good. However, sometimes they run across security that actually counterattacks their hacking, which might be something of an aversion (encryption that can scramble your brain? AWESOME).
Mythology Gag: Anna and Uni Puma show up as a couple of merchants in the streets of Etorofu. They get about 2 pages worth of dialogue. A Fuchikoma tries to barter with them for a piece of merchandise, but ends up accidentally stealing it when it ran off. Anna was pissed and grabs a machine gun, but Uni figures it was probably stolen merchandise in the first place anyway and says to just let it go.
The show up again in Human Error Processor in a crowd scene gawking at an explosion from a nearby apartment building.
Not What It Looks Like: Subverted by the threesome. While what's happening on the page is happening, underneath all that is an illegal, drug-enhanced data-sharing sim that uses the threesome as its interface.
Rule of Cool: Various footnotes explain that some of the vehicles are not drawn to scale, and that cyberspace wouldn't really "look" like anything - but it's cooler when it does. They even go so far to point out when a character's suggestions and line of thinking wouldn't actually work.
Sex by Proxy: Batou gets hit with this in-story. Aramaki orders him to contact Motoko and pull her off leave, so he proceeds to dive into her mind...while she's in the threesome. As noted elsewhere, it's not a pleasant experience for him. The scene got heavily censored in the original US release, but was included in the reprint (the page picture). Kodansha's latest version removes it entirely, but dialogue makes it clear what's going on.
Shout-Out: The Puppet Master plans to merge his mind with Motoko's and become the progenitor of a new species who would have godlike powers over cyberspace. This is reminiscent of Wintermute's plan to merge with Neuromancer.
Shown Their Work: The margins are crammed with Shirow's footnotes informing the reader that he knows very well that cyberspace doesn't look like that, and this plane wouldn't actually be that large, or that 16^2 refers to the size of the micromachines used for skin sensitivity, and not the amount of artificial nerve endings per square centimeters. The author notes at the end of the first manga shows he really REALLY did his homework with political, technological, theological, and philosophical themes presented.
Situational Sexuality: Heterosexual brainsex is impossible for biological reasons, so the Major's cyber orgy is with other girls. (Actually, Masamune just didn't want to draw a guy's butt.)
Spider Tank: The Fuchikomas, as well as the "German Spider Tank"
Squick: invoked Batou's reaction to the Sex by Proxy instance above. Having a male body, he's hit with sensory input which he has no nerve endings for, and it makes him feel very ill. In other words, he experienced a female orgasm in a male body.
Stripperiffic: Considering that this is written by Shirow Masamune, fans often forget that Maj. Motoko Kusanagi constantly wears sensible, concealing clothes. Motoko Aramaki, on the other hand...
Submarine Pirates: Motoko caught a bunch of pirates in a stolen Imperial American submarine sneaking under her clients' floating city. Fortunately she had a better sub.
Talking to Themself: All of the major female characters in Man-Machine Interface turn out to be offspring of Motoko Kusanagi and the Puppetmaster (the protagonist is number 11), and one of them is Kusanagi/the Puppetmaster.
Technology Porn: This series enjoys showing off the various technologies that the future has. The various forms of mecha as well as interacting through the net in particular.
Technical Pacifist: Aramaki is too old to do any fighting. He's always been the political leader of Section 9 who takes care of the paperwork, and doesn't have a violent bone in his body. However, when he learns that Section 1 was trying to hunt down and kill Motoko as part of a gambit they got caught up in, he pulls out a gun and cocks it right in the face of Section 1's leader without a second thought, ordering him to call off his men.
Unusual User Interface: Both the jacks used to access the web, the internal LAN's sometimes used to hack or get hacked, and even subverted by using normal keyboards. There's also talking in barcodes and laser communication by staring at people with Eye Beams.
Would Hit a Girl: Practically everyone, male and female. Togusa lampshades it after knocking down a woman attacking him, claiming that he believes in "equality for the sexes".
You Can Never Leave: The cyborgs of Section 9 require constant high-level maintenance, and there would be little left to resign once the government had taken back all its classified cyber-technology. As it turns out the Major discovers a way to Take a Third Option.