Hiniiru

Ten years ago, a black shape appeared in the sky and destroyed the city below. Kagerou and Momiji were children when the destruction took place, and they have grown together into teenagers beneath the mysterious structure. There is an undeniable attraction between these two friends, but Kagerou is hesitant to confess his feelings because he feels that he is too weak to protect her.

One day, the structure acts again, sending down strange balls that eat people and transform them into monsters. Kagerou and Momiji's encounter that day changes them forever. Kagerou is taken into an organization that explains to him that he is now an "ember," and Momiji is a non-human "dross," useful only as experimental material. Kagerou can't accept this, though, and is determined to do anything in his power to protect the girl he loves.

(Source: MangaHelpers)