Comet Lucifer tells the story of the planet Gift, a land covered by Gift ore, a mineral that shines with blue light. Sougo Amagi is a simple boy who lives in Indigo Garden, a town that prospers due to the mining of Gift ore. Sougo, who enjoys collecting rare ores, is caught up in the commotion caused by his classmates Kahn, Roman, Ott and others one day and gets lost in the underground lake deep in the mine. There, Sougo meets an incredible girl with long blue hair flowing in the wind and red pupils staring straight at him. Who is she and what does this encounter bring to Sougo? Then, the bond that is established will open the door to adventure.