A massive anomaly caused a great earthquake that ravaged Japan's mainland and destroyed most of Tokyo, sinking three-quarters of the city into the Pacific Ocean.
Ten years later, the story shifts to Ganta Igarashi, a seemingly ordinary student attending Nagano Prefecture's middle school. As an escapee, a survivor of the great earthquake, Ganta has no memories of the tragedy and has lived a normal life. This all changes when a strange person covered in blood and crimson armor floats through his classroom windows. Grinning madly, the "Red Man" massacres Ganta's entire class. Instead of killing him, the "Red Man" embeds a red crystal shard in Ganta's chest.