Losing a loved one is so painful that one may sometimes wish to be able to resurrect them—a weakness that the enigmatic Millennium Earl exploits. To make his mechanical weapons known as "Akuma," he uses the souls of the dead that are called back. Once a soul is placed in an Akuma, it is trapped forever, and the only way to save them is to exorcise them from their vessel using the Anti-Akuma weapon, "Innocence."

After spending three years as the disciple of General Cross, Allen Walker is sent to the Black Order—an organization comprised of those willing to fight Akuma and the Millennium Earl—to become an official Exorcist. With an arm as his Innocence and a cursed eye that can see the suffering souls within an Akuma, it's up to Allen and his fellow Exorcists to stop the Millennium Earl's ultimate plot: one that can lead to the destruction of the world.

D.Gray-man is based on Katsura Hoshino's manga series of the same title. The anime adapts the first 158 chapters from the first 16 volumes, while adding anime exclusive content, mainly during the first half of the series.

FUNimation Entertainment licensed and released only the first 51 episodes of D.Gray-man. The explanation they provided for not acquiring the remaining episodes was that there were licensing issues with Dentsu. However, on June 30, 2016, it was announced that Funimation acquired the rights the second half of the anime.