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It found a voice... now it needs a body.
My thoughts as to what Ghost In The Shell is really about.
I think when Ghost In The Shell was first conceived as an idea it was really just a vehicle to have a sexy female main character in a futuristic robotic world. Most, if not all, comics written by Masamune Shirow have a female lead. It's no coincidence that Motoko is sexy, has large breasts, and is openly bi-sexual in the comics. But as the story developed it's ended up being a lot more than that. There's a deeper meaning to the stories than just a sexy female cyborg kicking ass.
Motoko has a human brain inside a brain case that's been placed inside a cyborg body. There are gaps in her memory and she isn't sure that they haven't been manipulated. Obviously she has never seen her own brain and cannot be sure if she's a total cyborg programmed to think that it started as human, or whether she did in fact start out as human but has been given fake memories. Soldiers from the previous world war were experimented on including Batou who had his eyes replaced so it is very possible that the government did cyborg experiments too. Cyborgs, and even regular human beings, can have their minds hacked so it's more than possible Motoko isn't who she thinks she is.
It's also possible for cyborg minds to leave their body and live in cyberspace on the net or change to another cyborg body completely, although this may be a form of hacking by Motoko rather than her mind physically leaving her body. It is unclear in the comic books.
There's a kind of uneasiness about the idea that humans and machines are essentially the same and can both have there minds wiped and reprogrammed. In one of the comics a police woman with a cyborg hand has her control software updated making her hand more efficient, but rather than be pleased she is actually angered preferring her hand to be slow again keeping it more human.
The story shows the advantages there can be when machines and humans become more integrated, but it also points out the many disadvantages too.