The Gems, crystalline creatures, live in a post-apocalyptic world where six meteors have wiped out much of life. They are constantly under attack by the Lunarians who seek to use the Gems' bodies as decorations. Phosphophyllite, or Phos, desires to contribute in the battle effort but is limited by their delicate nature. Instead, they are assigned the task of compiling an encyclopedia. It is during this undertaking that Phos encounters Cinnabar, a bright Gem whose toxic body has restricted them to night patrolling on a remote island. Sympathetic to Cinnabar's misery, Phos sets out to find a purpose that both Gems can enjoy. Houseki no Kuni shows Phos' journey to protect their fellow Gems and make a difference in the world.