 If you liked
Noein: Mou Hitori no Kimi e
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 ...then you might like
Darker than Black: Kuro no Keiyakusha
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Both involve high technology, plenty of battles and a somewhat dark storyline.
In DtB, Hei is somewhat related to an incident resulting in the disappearance of South America. Similiarily, in Noein, Karasu is distantly related to the disappearance of various alternate worlds. Both protogonists are capable fighters, and both are searching for what happened in past times.
Both: sci-fi, superpowers, antiheroes, secret organisations
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Recommended by ThePoliyoyo