The foolish humans, whose hearts are filled with darkness, have lost the light in their eyes. Trapped within that darkness, they can no longer find their way. Crushed by despair, these humans one day meet the hotaru, which carry a faint, warm light. The hotaru provided humans with that light and began living alongside them. But in this ugly, bloodstained world, the number of hotaru decreased day by day. Yet the humans, still desiring the light, started hunting the hotaru, throwing away their lives for money. Nemu, a hotaru who has lost her light, makes a contract with an abandoned baby named Haibane. Haibane searches for a way to restore Nemu's light.