Set in an alternate 19th century Europe, an enigmatic entity known as the Earl of Millennium is striving to bring about the downfall and destruction of mankind to cleanse the world reminiscent of Noah's great flood. He has an army of Akuma at his disposal, merged creatures of soul and machinery. Defied by the members of the dark Religious Organization, The Black Order, they are the protectors of humanity. They are the Exorcists. These are gifted individuals, granted the power to use the Innocence, the ultimate weapon against the Akuma.
This world of D.Gray Man has unified right before the events that took place with the landing on the coast of Japan by the Exorcists in search of General Marian Cross. Things deviate from that point as the unification occurs and the Earl packs up his plan to hunt down the Generals and withdraws to the Arc, sealing it away as he moves to investigate the shift in the world's nature and the stranger nature of the Multiverse.