In a mysterious future, crystalline beings known as Gems inhabit a world devastated by six meteors. Each Gem is assigned a specific role to fight the Lunarians, a species that attacks them to shatter their bodies and use them as decorations. Phosphophyllite, also known as Phos, is a young and fragile Gem who dreams of aiding their friends in the war effort. Instead, due to their delicate condition, they are ordered to compile an encyclopedia. After reluctantly starting this task, Phos meets Cinnabar, an intelligent Gem who has been relegated to patrolling an isolated island at night because of the corrosive poison their body produces. Seeing how unhappy Cinnabar is, Phos decides to find a role that both rejected Gems can enjoy. Houseki no Kuni follows Phos' efforts to be useful and protect their fellow Gems.