Evil Genius

This anime is right up there with Berserk for me. I would say some aspects are darker than berserk and it really toys with your morals. I highly suggest watching it!
It took me awhile to actually start watching this, the animation is late 90's era so if you can get past that I think you'll enjoy it.

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i wouldnt compare it to berserk, but i really liked it as well. it felt more like a non mecha rahxephon from what i recall. anyhow i also recommend it