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In the distant future, a new immortal and genderless life form called Gems populate the Earth. The 28 Gems must fight against the Moon Dwellers, who attack them regularly to abduct them and to turn them into decorations. Each Gem is assigned a role, such as a fighter or a medic. Being only 300 years old, Phosphophyllite is the youngest of the Gems and has no assignment yet. He wants to help to fight the Moon Dwellers, but is too weak and brittle for battle. One day the master of Gems, Kongou (Adamantine), assigns him the task of creating a natural history encyclopedia.

In the mysterious future, crystalline organisms called Gems inhabit a world that has been destroyed by six meteors. Each Gem is assigned a role in order to fight against the Lunarians, a species who attacks them in order to shatter their bodies and use them as decorations. Phosphophyllite, also known as Phos, is a young and fragile Gem who dreams of helping their friends in the war effort. Instead, they are told to compile an encyclopedia because of their delicate condition. After begrudgingly embarking on this task, Phos meets Cinnabar, an intelligent gem who has been relegated to patrolling the isolated island at night because of the corrosive poison their body creates. After seeing how unhappy Cinnabar is, Phos decides to find a role that both of the rejected Gems can enjoy. Houseki no Kuni follows Phos' efforts to be useful and protect their fellow Gems.