Long ago, Earth was struck by six meteorites, creating six moons and leaving a lone island in their wake. Those who could not make it to the island sank to the bottom of the ocean, where, over time, they slowly turned to crystal. As countless millennia passed, 28 of these crystallized lifeforms, known as the Lustrous, rose from the depths and resided on the island. Led by the wise Kongou-sensei, they must defend themselves against the seemingly infinite number of Lunarians, inhabitants of the moons who seek to harvest their valuable bodies for crafting weapons and jewelry.

Houseki no Kuni centers around Phosphophyllite, a young gem about to turn three hundred years old. Clumsy, extremely fragile, and having no visible talent, they are one of the weakest gems around, unable to help in the fight against the Lunarians in any meaningful way. But as the battle with the otherworldly invaders rages on, they soon learn that power comes at a cost that no one should have to pay.