After her parents were brutally murdered, school girl Sawa was taken into custody by Akai and Kanie, a pair of detectives assigned to her case. Corrupt and immoral, they train the girl to become a weapon, dangling the promise of vengeance in front of the hapless orphan. From celebrities and politicians to influential businessmen, Sawa is tasked with assassinating targets selected arbitrarily by her crooked overseers. She executes every mission without fail, and her distinctive weapon has become infamous among the city's police officers. Physically abused by Akai, who is no more righteous than her victims, Sawa begins to dream of a life unhindered by the shadow of her "guardians." One day, Sawa meets Oburi, a fellow orphan and vigilante. They quickly form a bond born of desperation and disgruntlement at the unjust world, envisioning a future free from the stain of murder.

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. [Written by MAL Rewrite]

While the perfect getaway for most girls her age might be a fancy vacation with their loved ones, Rin Shima's ideal way of spending her days off is camping alone at the base of Mount Fuji. From pitching her tent to gathering firewood, she has always done everything by herself, and has no plans of leaving her little solitary world. However, what starts off as one of Rin's usual camping sessions somehow ends up as a surprise get-together for two when the lost Nadeshiko Kagamihara is forced to take refuge at her campsite. Originally intending to see the picturesque view of Mount Fuji for herself, Nadeshiko's plans are disrupted when she ends up falling asleep partway to her destination. Alone and with no other choice, she seeks help from the only other person nearby. Despite their hasty introductions, the two girls nevertheless enjoy the chilly night together, eating ramen and conversing while the campfire keeps them warm. And even after Nadeshiko's sister finally picks her up later that night, both girls silently ponder the possibility of another camping trip together.

The anime series will adapt 20 stories from a number of Itou's manga for the first time, including Tomie, Souichi, and Kubitsuri Kikyuu (The Hanging Balloons).