Subaru is a young girl who likes to see the stars. One day, she opens the door to her school's observation room, only to find a large indoor garden instead! She meets a boy named Minato who says some strange things, telling her to leave soon after their meeting. As if the day wasn't weird enough, Subaru accidentally finds a strange blobby creature who runs off with her compass, leading her to stumble into a club room with girls wearing witch costumes! Subaru recognizes her friend Aoi in the group, and despite Aoi's protests, Subaru decides to join the club. Shortly after, she gets a strange automobile-like staff and a magical transformation from the club's president, the blobby creature from earlier, known as a Pleiadian. Aoi and the other members—Itsuki, Hikaru, and Nanako—have been looking for engine fragments of the spaceship that the Pleiadian used to travel in, so that it can go back to its home. But it seems that these girls are not the only ones searching for the fragments...

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.

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.