 If you liked
Shinseiki Evangelion
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 ...then you might like
Ga-Rei: Zero
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Both have large secret government organisations as the protagonists trying to defend the world against strange beings. Both are tragic as many things go wrong and each look at the main characters inner flaws and subsequent conquering (Yomi’s inner resentment of Kagura and shinji’s cowerdice). Both of these are extremely well made stories with a great mix of action and plot.