 If you liked
Koukaku Kidoutai: Stand Alone Complex
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 ...then you might like
Death Note
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Dig out your sleuth hats. Both series follow a plot that is very challenging to figure out. While Ghost in the Shell has a greater focus on action, Death Note and GitS share the ability to baffle with plot twists and complex schemes.
Both series' stories involve very deep, intellectual concepts and the plot twists, in particular, are amazing. While GitS has far more filler than Death Note, both series almost always focus on crime and/or the psychology and rationale of the people who drive the stories forward. Also, they both have absolutely stunning art styles.