In the depths of a labyrinthine ruin, a young girl named Mion rises from a deep sleep. Lost, alone, and with no memory of how she got here or where her parents are, she is greeted by two fireflies—one composed entirely of light, and another who lurks among the shadows. By shifting between a world of light and a world of shadows, these two fireflies must work together to recover Mion’s memories and lead her out of the ruins, where voracious shadow beasts, ancient machines, and treacherous traps lie in wait to bar her path.

The story begins on December 31, 9999, when a young amnesiac girl by the name of Mion wakes at the bottom of a dark ruins within a desolate world. Following a desire to let Mion escape the rubble and see the outside world, the firefly Hotaru leads her on a journey upwards through the ruins. On her journey outwards, she finds unmanned machines, distorted vegetation, and bodies of dead children.