Almost every scene is recreated or referenced from start to finish from the original manga across the series.
- The second episode of the first season has a robot tank that has a crippled soldier's brain uploaded to it go on a rampage to his anti robotics parent's house. Kusanagi attempts to stop it by ripping open it's hatch just like the climatic battle in the film. In this case it doesn't result in Explosive Overclocking and she doesn't rip herself apart, she just doesn't have the strength to do it.
- In the SAC episode DECOY, Motoko goes to a friends house to use a device to help her learn more about the Laughing man. The scene is a "sanitized" shout out to the infamous "Lesbian Boat Scene" in the manga.
- In MISSING HEARTS, Batou challenges Motoko to a fight and she responds by hacking him and causing him to punch himself in the face. This is a reference to her doing the same thing to him when he accidentally accessed her sensory feeds during the same scene in the manga.
- There's a recreation of a scene where Pazu interviews someone, asking for the current face and name of a person they're looking for, all while remaining invisible throughout the conversation, then departing with a comment on how it must be nice to be a Desk Jockey.
- In episode 25, there is a reference to the scene in the film with Motoko/Puppetmaster's new body, only this time with Motoko's younger-self puppet in her high-rise safehouse.
- The fight between the Major and a Powered Armour-wearing Gayle in ERASER is an almost blow-by-blow recreation of her fight with the Spider Tank in the first movie. At the end, Saito even shows up with an anti-tank rifle the way Batou did in the original scene.
- The first episode of 2nd Gig mimics the iconic shot of Motoko diving off a building and becoming camouflaged from the first chapter of the manga (later the opening sequence of the movie), then shooting a man to end a confrontation as she falls past his window, though in a slightly simpler style (and minus the movie's nudity). A different part of the scene, Motoko shooting the target to Ludicrous Gibs on orders of the prime minister, is used in the series finale.
- In the 3rd episode of 2nd GIG, one of the sex dolls in the background looks just like the Major in her civilian clothes from the manga.
- For a few episodes in 2nd Gig, Batou is wearing his beige jacket from the original movie.
- In the second season, Batou exclaims that dogs don't like him much.
- 2nd Gig's denouement is almost a word-for-word, shot-for-shot reproduction of the start of the manga's second chapter, with the team in lighter-colored uniforms with more prominent padding, watching cherry blossoms and waiting for an increased budget. The only difference is Motoko's personality (she's the mature Mother To Her Men commander of the anime instead of the bitchy Heroic Comedic Sociopath she was at that point of the manga). ** Also in 2nd Gig, the second episode's ritzy sex party has an unmistakable Puma Sister of DominionTankPolice, in her New Dominion OVA attire, complete with long orange hair, red swimsuit and spiked bracelets, on display behind glass. In the original manga, Dominion and Ghost in the Shell share continuity to the point where both Puma Sisters briefly encountered Section 9.
- During a standoff in 2nd Gig, Batou shoots a cornered refugee girl in the mouth to keep her from triggering an explosive wired into her jaw. This is lifted from one of Shirow's other works, Appleseed, which takes place in the same continuity as GITS.
- Much of the Etorofu episode in 2nd Gig was largely lifted from the manga, including the cyborg Koil, the geofront and the visit to Sagawa Electronics.