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Not only does Motoko not have a real ghost - No one does!
The entire Ghost in the Shell series takes place in a world where humans haven't existed for a long time - possibly centuries. Those who believe themselves to be full-body prosthetic cyborgs are actually androids, built and programmed from scratch. The few characters we see with definitely biological parts aren't late adopters who haven't yet replaced their bodies - They're the latest generation in an ongoing attempt to finally bring back the human species. The fact that, even these mostly biological characters still have some degree of augmentation (like Ishikawa, Togusa, and Saito) is actually due to the fact that the bio-rebirth program is still incomplete. The synthetic-organic tissue is unstable without cybernetic augmentation.
The world of Ghost in the Shell: Stand Alone Complex is set on earth in the Transformers universe after the Transformers had left earth.
After the autobots had won the war on earth they left for Cybertron leaving a litter of Decepticon slag behind them. A few human scientists picked the dead transformers up and experimented with their core personality units to find out how to conserve the human brain with such technology.
After a lot of experiments they came up with the first cyborg thanks to the Transformers.
The world of Ghost in the Shell: Stand Alone Complex is not earth.
It's the home planet of the Borg from Star Trek, but in a distant past, when the development of cyber technology had just begun and the hive mind had not yet developed, but certain smaller pre-forms of it (like, for example, the Gestalt of the old people in Solid State Society) were already around. Motoko Kusanagi will eventually become the first incarnation of the Borg Queen.
In the GITS world, Russia, and some of its neighbors, are part of a Eurasian Union State
The original GITS manga, like 'Appleseed', assumes the continued existence of the USSR—though not geographically as large as it was in, say, 1985, due to World War (practically no country is). The TV series explicitly refers to the SVR, an institution that emerged as a direct result of the August Coup that led to the transformation of the USSR into the CIS. However, there are still references to 'the Soviets'—by Kayabuki referencing the 'American-Soviet Alliance', the third player in North American (the other two being the remaining United States and the American Empire), interchangeably described as 'Russo-American Alliance' as well. It's a recognition of a tendency in the capitalist world to have use to do the same thing. In Stand Alone Complex, the formation of the CIS did happen at some point, but was later followed by a further supranational union (an extension of what exists in the real world), certainly between Russia, Belarus, Ossetia, and Abkhazia, and possibly included Armenia, Kazakhstan, Turkmenistan, Uzbekistan, Tajikistan, Nagorno-Karabakhand, and perhaps Mongolia and Ukraine. "Soviets" simply means "council" in Russian, so if the the Union State is a parliamentary supranational federation, it's still 'technically' correct, and it might be more convenient, and familiar, than "Eurasian Union of Republics".
The Major was a test subject in the Japanese version of the program used to create the cyborgs of Gunslinger Girl.
Think about it. She was a little girl who suffered injuries when she was very young. Then she was taken away and turned into a cyborg who now works for the Government and is very skilled in combat. It is very likely that being a full cyborg she didn't suffer the effects of the conditioning which lead to death and it is also likely that didn't need a handler now that she can work on her own.
Ghost In The Shell is the near future of Evangelion.
Think about it. It's set fifteen years after Eva(at least the anime is), there has been mention of a war that obviously had an effect on technology and society world-wide, and souls are relatively easy to transplant into machines.
Obviously, Instrumentality failed spectacularly in that everyone came back quickly, possably that day, and all the prosthetic body parts and mechs could easily come from commercialization of equipment from Project E. The reason Shinji and Asuka are never mentioned or seen is because after Third Impact and Instrumentality, they voluntarily went into hiding, and are probably living contently in some remote location.
The reason there are so few WMGs for this show is because the Major is hacking the site and deleting them all, because so many of them happen to match classified material.
This naturally requires time travel.
The Ghost in the Shell franchise is the Spiritual Successor to three unleashed Cyberpunk thrillers that were tragically mis-categorized as children's movies, thus annihilating any adult appeal: The Brave Little Toaster, The Little Mermaid, and All Dogs Go to Heaven.
Aoi is the son of L.
Prime Minister Kayabuki is of Chinese ancestry.
The Prime Minister's surname (芧葺, meaning 'reed thatch') doesn't make much sense as a Japanese name, except as a nod to Margaret Thatcher. However, in Chinese, the character 芧, which means approximately the same thing, is also used as a surname, indicating that either the Prime Minister or her family could have changed their name to a Japanese word with the same meaning as their Chinese name upon emigrating. Also, her character design is very similar to that of Fem, the South Chinese hit(wo)man in the episode Full Auto Capitalism; ¥€$, especially around the eyes and in the skin tone. Finally, Kayabuki's dialogue at certain points in the series indicates that she has some sort of odd attachment to China, which seems strange considering that China and Japan haven't been on the best of terms through the past several decades, and that the Chinese government is actively making her job more difficult by escalating the problem of the growing refugee population. Since Japan doesn't have any law against foreign-born people serving as the prime minister, it's entirely possible that she was born in China or grew up there, explaining her implied wistful desire for things to be better between the two countries.
Borma's obese appearance is due to massive amounts of subdermal armor and padding.
It's rather odd that a full-body cyborg would want to appear borderline morbidly obese, especially in paramilitary duty, when it came to him: Borma mentions during the 2nd Gig that he used to rig and dismantle bombs for the army, so his physiology would be designed specifically for that purpose. He is built to endure the blast of an explosion far better than a normal cyborg ever could.
Batou is gay, but also in love with the major
That's why he wants her to swap out to a male body — so he can resolve that conflict.
At some point, Major Kusanagi swapped her old cyberbody for a new one.
This explains why she looks different in the show versus the movie. When her body was destroyed trying to rescue the Puppet Master, her ghost was transferred into the body of a little girl (which is how we see her in the final scene of the movie) but when she went back to work for Section 9, she opted for a different model with purple hair and red eyes, just because she thought it'd look cool. And how's this for Fridge Brilliance - her ghost merging with that of the Puppet Master explains why her personality is somewhat different in the show than in the movie. To support this version of events, note that the movie takes place in 2029 but the show does in 2030.
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