 If you liked
Darker than Black: Kuro no Keiyakusha
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 ...then you might like
Mahouka Koukou no Rettousei
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Both have dark haired cool (or cold, choose) main hero with hidden identity and "secret job", who is overpowered. There are also some imouto issues, lot of stereotypical side characters and running away from past.
The similarity in setting: It's postapokalyptic, there are two types of people (contractors and magicians vs. "normal") and there is significant military involvement.