 If you liked
Shinseiki Evangelion Movie: Air/Magokoro wo, Kimi ni
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 ...then you might like
Serial Experiments Lain
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Science fiction titles from the 1990s that delve into the minds of their adolescent protagonists. They are also very cerebral and have some nightmarish imagery.
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Recommended by LoveLikeBlood
Both feature a young, shy, possibly mentally ill, yet deeply flawed protagonist who is desperate for connection with others. Due to circumstances beyond their control involving advanced technology, they end up having to make choices affecting the fate of themselves and many others, and struggle with the selfish choice versus the morally correct choice. Both works have a reputation of being excessively confusing but make sense when you realize it's the ideas that matter, not a literal interpretation of what exactly happened on-screen.
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Recommended by kerberos242