Allen Walker, a young man with a cursed eye, lives to destroy a weapon known as Akuma. These weapons created by the Milleneum Earl are sent out by his command to purge the world from humans. Allen Walker uses an anti-akuma weapon, Innocence, to counter the Earl's attempts at destroying humanity. He travels to the Black Order by his mentor's directions. There he meets with others who also fight against the Milleneum Earl's plans. But more questions start to appear as Allen and his friends move further along to reach their goal. And these questions that seem to connect to Allen's past.

D.Gray-Man - Box 2 end:

• 53. Fallen One
• 54. The Beginning of the Night's End
• 55. Scream
• 56. Delete
• 57. Disappearance and Reunion
• 58. The Asia Branch
• 59. The Road of an Oath
• 60. Title
• 61. Sinking Darkness
• 62. A Holy Woman Fallen Into Darkness
• 63. The Girl of the Ship That Didn't Return
• 64. Message
• 65. Landing
• 66. Disturbance and Impatience
• 67. To Edo
• 68. Silence
• 69. Invasion
• 70. God's Clown
• 71. The Signed Name
• 72. Decisive Battle in the Imperial Capital
• 73. Kanda, Engages in Battle
• 74. Edo's Annihilation
• 75. Clown and Auguste
• 76. Key and Noah's Door
• 77. Skin Bolic Room
• 78. Taboo, Three Illusions
• 79. Noah's Memory
• 80. The Twins' Trap
• 81. Debt Crisis
• 82. Bad Game
• 83. Jasdevi, Enter
• 84. Bloody Krory
• 85. Dark-Colored Rhapsody
• 86. Weak Person
• 87. Critical Point
• 88. Lavi
• 89. The Voice of Darkness
• 90. Black Carnival
• 91. Judgment
• 92. The Musician's Shadow
• 93. Melody
• 94. Homecoming
• 95. The Sheep and the Dog
• 96. Yet the Hands of Time Move Onward
• 97. Headquarters Under Siege
• 98. The Power of the Generals
• 99. Noah of Lust
• 100. Level 4
• 101. To the God I Hate
• 102. Words of Promise
• 103. Resounding in long morning