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.

Now in his second year of high school, Rei Kiriyama continues pushing through his struggles in the professional shogi world as well as his personal life. Surrounded by vibrant personalities at the shogi hall, the school club, and in the local community, his solitary shell slowly begins to crack. Among them are the three Kawamoto sisters—Akari, Hinata, and Momo—who forge an affectionate and familial bond with Rei. Through these ties, he realizes that everyone is burdened by their own emotional hardships and begins learning how to rely on others while supporting them in return. Nonetheless, the life of a professional is not easy. Between tournaments, championships, and title matches, the pressure mounts as Rei advances through the ranks and encounters incredibly skilled opponents. As he manages his relationships with those who have grown close to him, the shogi player continues to search for the reason he plays the game that defines his career.

Daisuke Kanbe, a man of extraordinary wealth, is assigned to the Modern Crime Prevention Headquarters as a detective. It is there that he gets partnered with Haru Katou, a humane detective who values justice above all. The two are polar opposites, and their morals clash time and time again. Haru despises Daisuke for using monetary wealth to solve cases, as he believes that money isn't everything. The two will have to combine their efforts, however, to solve the mysteries that are coming their way.

Humans have designed countless worlds—each one born from the unique imagination of its creator. Souta Mizushino is a high school student who aspires to be such a creator by writing and illustrating his own light novel. One day, while watching anime for inspiration, he is briefly transported into a fierce fight scene. When he returns to the real world, he realizes something is amiss: the anime's headstrong heroine, Selesia Yupitilia, has somehow returned with him. Before long, other fictional characters appear in the world, carrying the hopes and scars of their home. A princely knight, a magical girl, a ruthless brawler, and many others now crowd the streets of Japan. However, the most mysterious one is a woman in full military regalia, dubbed Gunpuku no Himegimi, who knows far more than she should about the creators' world. Despite this, no one knows her true name or the world she is from. Meanwhile, Souta and Selesia work together with Meteora Österreich, a calm and composed librarian NPC, to uncover the meaning behind these unnatural events. With powerful forces at play, the once clear line between reality and imagination continues to blur, leading to a fateful meeting between creators and those they created.