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her female body is nothing but a physical tether that constrains her own individuality.

I also think this is hinted at when the puppetmaster’s seemingly male voice speaks through Motoko’s body, and is finally realised when Motoko acknowledges that there is no longer any woman called the major, nor an entity called the Puppetmaster: she has transcended beyond the physical limitations of biological sex and is now a genderless, free being.

It’s a very powerful and interesting film and this is just my reading, but I’ve seen so many differing interpretations, which makes me appreciate just how brilliant a work of art it is.