Set in a fictional 19th century England, D.Gray-man is the story of Allen Walker, a 15-year-old boy who roams the earth in search of Innocence. Washed away to unknown parts of the world after The Great Flood, Innocence is the mysterious substance used to create weapons that obliterate demons known as akuma.

Allen has disappeared. Lavi and Lenalee rush to find him, only to wind up confronting a horde of akuma pursuing Allen's golem Timcanpy. After dealing with this they are ordered to continue their mission without Allen, his place to be taken by a new Exorcist--Miranda Lotto. Allen, meanwhile, wakes up inside the Asian Branch of the Black Ministry to the sobering reality that he has lost his Innocence!