Hina Tsurugi and her family have just moved to a quaint seaside town. Hoping to savor the sight of the peaceful ocean, Hina stumbles upon a girl named Yuuki Kuroiwa—an upperclassman at her new school—who invites Hina to join her in fishing. Hina reels in an octopus, which falls onto her; being afraid of bugs and big creatures, she panics and begs Yuuki to remove it from her. Yuuki sees this as an opportunity to force Hina to join the school's Breakwater Club—a club where members gather, catch, and eat various types of marine life as their main activity. Although her attempts to refuse to join fail, Hina slowly begins to discover the hidden joy in fishing. Her view on the sport changes, now looking forward to all the delightful experiences she can take part in alongside her fellow club members.

Possessing a deep knowledge of mineralogy, Richard Ranashinha de Vulpian is a young and handsome British jewelry appraiser who owns a small shop in Japan. One fateful night, Seigi Nakata, a righteous college student, saves him from drunks who were harassing him due to his good looks. Upon learning of Richard's identity, Seigi hires him to appraise a pink sapphire ring that was left behind by his deceased grandmother. Before long, Seigi becomes a trusted part-timer at Richard's shop. Together, the duo solve various jewel-related requests from diverse clients of different backgrounds. Step by step, they unravel the hidden motives and feelings that lie within the gems in order to understand and empathize with the little stories behind each piece of jewelry.

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.

As the first commoner to attend the prestigious Arnold Academy of Sorcery, Ray White is immediately met with contempt from some of the students hailing from nobility. Unbeknownst to them, Ray's real identity is that of the famous Iceblade Sorcerer—a hero who led the country to victory in a past war and is one of the seven strongest sorcerers alive. Despite his legendary status, Ray wants nothing more than to live out the ordinary school life he never had. Ray quickly makes friends with some of the most influential students thanks to his kind and amiable nature. Unfortunately, as those with nefarious motives begin to make their move, Ray may soon have no choice but to use his true power to preserve the bonds that make his new life worthwhile.