The foolish living things, the humans, who carry darkness in their hearts, lost the light from their eyes.

Deep inside the darkness, they lose sight of the way. Crushed in their despair, the humans one day meet creatures called the hotaru who each carry a faint, warm light. The hotaru provided the humans with the light, and started to live alongside them. But in this ugly and blood-stained world, the hotaru's number started to decrease day by day. Yet, the humans wanted the light and started to hunt the hotaru. For money they would throw away the life of a hotaru.

Nemu, a hotaru who has lost her light, makes a contract with a abandoned baby, Haibane. Haibane seeks to find a way to gain back Nemu's light.