Haibane Renmei follows Rakka, a young Haibane who wakes from a cocoon in Old Home with a halo, small gray wings, and no memory of who she was before. Given her name from the dream of falling she had inside the cocoon, she gradually learns the quiet routines of the village and the town beyond it, where the Haibane live under rules they do not fully understand. They are forbidden to leave the village or approach the walls that surround it, and each one must eventually face the mysterious Day of Flight, when a Haibane simply disappears. Those customs leave Rakka and the others uneasy, because they know almost nothing about their own kind or the fate that waits for them.
As Rakka becomes part of daily life in Old Home, she and the other Haibane try to make sense of their missing memories, the pain that still lingers beneath the surface, and the fragile hope that they can break free from the burdens of their former lives. Haibane Renmei slowly builds a contemplative portrait of loneliness, companionship, and the search for meaning in a strange, enclosed world.