Effeminate fifth grader Shuuichi Nitori is considered by most to be one of the prettiest girls in school, but much to her dismay, she is actually biologically male. Fortunately, Shuuichi has a childhood friend who has similar feelings of discomfort related to gender identity: the lanky tomboy Yoshino Takatsuki, who, though biologically female, does not identify as a girl. These two friends share a similar secret and find solace in one another; however, their lives become even more complicated when they must tread the unfamiliar waters of a new school, attempt to make new friends, and struggle to maintain old ones. Faced with nearly insurmountable odds, they must learn to deal with the harsh realities of growing up, being transgender, relationships, and acceptance. Lauded as a decidedly serious take on gender identity and LGBT struggles, Takako Shimura's Hourou Musuko is about Shuuichi and Yoshino's attempts to discover their true selves as they enter puberty, make friends, fall in love, and face some very real and difficult choices.

There are rumors that one of Kamome Academy's Seven Mysteries, Hanako-kun, has gained an assistant: first-year high school student Nene Yashiro. Together, Hanako and Yashiro investigate the school's many mysteries, keeping the balance between humans and the supernatural. But in their free time, the two can often be found goofing off, engaging in various antics involving Yashiro's schoolmates and the lurking spectral entities that normal people cannot see.

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.

Masanosuke Masa Akitsu is a wandering ronin adrift in Japan's peaceful Edo period. Despite being a skilled swordsman, Masa's meek personality has netted him the label unreliable, and he is often abruptly dismissed by his employers, leading him to question his resolve as a samurai. As Masa reaches his lowest point, he is approached by Yaichi, a carefree man draped in pink who seemingly hires him on a whim as his bodyguard. Unbeknownst to Masa, the job is not as innocent as it seems, and he is drawn into the illicit activities of the group spearheaded by Yaichi. As he becomes further entwined with the gang known as the Five Leaves, Masa struggles with his own principles. Still, his curiosity spurs him forward to uncover the past and motivations of this mysterious band of outlaws.