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Yoite from Nabari No Ou presents as a male (albeit one who is described as “beautiful” and having long eyelashes), and male pronouns are used throughout the majority of the story. But about halfway through you find out he is “neither male nor female” and this gender confusion may have contributed to his sense of having no place in the world.

Aside from that, being intersex has no baring on the story itself. We are left to enjoy the wonder that is Yoite:

-has mastered a deadly ninja art and is widely feared at the beginning of the story

-goes through an astounding character transformation that quite honestly I think is one of the highlights of the whole story

-has a relationship with one of the other main characters that is one of the most amazing and heartbreaking of any manga I’ve read

Nabari No Ou just finished up this month, and at 72 chapters, is something that you could read fairly quickly. The hard part is – if you don’t read Japanese – finding scanlations and translations, since only four volumes have been published in English at this point. I would suggest mangahelpers and the LJ community as a starting point for finding additional chapters.