The ghostly Hanako-kun and his mortal assistant, Nene Yashiro, usually have their hands full resolving various supernatural incidents in Kamome Academy, but how do they spend their time when they get a break from all that? Come and watch the characters of Toilet-bound Hanako-kun play games, get sick, change genders, and discover world-shaking secrets during their laid-back after-school hours!

The ghostly Hanako-kun and his mortal assistant, Nene Yashiro, usually have their hands full resolving various supernatural incidents in Kamome Academy, but how do they spend their time when they get a break from all that? Come and watch the characters of Toilet-bound Hanako-kun play games, get sick, change genders, and discover world-shaking secrets during their laid-back after-school hours!

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First year student Hina Tsurugi prefers to do indoor activities such as crafting. Having recently moved to a seaside town, she runs into an older schoolmate, Kuroiwa, who invites her to join the "Teibou" club and start fishing! Surrounded by eccentric club members, how will Hina's high school life turn out?

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.

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Shuicihi Nitori appears to be a shy and quiet preteen boy, when he transfers to a new school he quickly makes friends with the tomboyish Yoshino Takatsuki who sits next to him. It soon becomes apparent that both Shucihi and Yoshino are more than simply a sensitive boy and masculine girl, they both are transgendered. Together they decide to take the first steps toward becoming the people they want to be.

The full versions of episodes 10 and 11 that were previously edited together into episode 10 of the TV series.

Masterless samurai Akitsu Masanosuke is a skilled and loyal swordsman, but his naïve, diffident nature has time and again caused him to be let go by the lords who have employed him. Hungry and desperate, he becomes a bodyguard for Yaichi, the charismatic leader of a gang called “Five Leaves.” Although disturbed by the gang’s sinister activities, Masa begins to suspect that Yaichi’s motivations are not what they seem. And despite his misgivings, the deeper he’s drawn into the world of the Five Leaves, the more he finds himself fascinated by these devious, mysterious outlaws.

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.

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.

The novel follows Richard Ranashinha Dvorpian, a handsome British jewelry appraiser, and Seigi Nakata, a bright and upright Japanese college student. The duo solves various jewel-related cases by unraveling the hidden psychological aspects of their owners that lie within the gems.