When a mysterious entity suddenly appears in the center of Tokyo, the Alta Mira Agency is tasked to repel the extraterrestrial threat. Otsuya Funagai must guide his all-female unit of Battle Sole pilots to take down the strange being no matter the cost. However, his intimate relationship with one of the pilots, Rin Ichikawa, may spell trouble for the team and the mission itself.

The story revolves around Yuuki Kagami, a boy who enrolls in the academy of his dreams as a honors student — and is mistakenly put in the girls' dormitory where boys are prohibited. Faced with the possibility of having to leave the school, Yuuki has to dress up as a girl in the dormitory. On top of things, he ends up rooming with the female teacher Ayana Kakinozaka, who has to watch over him.

Far in the future, where interstellar travel is considered commonplace, high school student Marika Katou balances her duties in the space yacht club and her job as a restaurant waitress. Following a chance encounter with a peculiar pair of customers, Marika meets them again and learns that her absent father has passed away. During his life, he was known as the legendary pirate Gonzaemon. He has left behind his infamous ship Bentenmaru and its crew exclusively for Marika to inherit. With one of the few remaining Letters of Marque that permit legal piracy, Marika must choose whether to stay as a regular student or take up a second life as a high-octane space pirate. As Marika ponders her decision, the delicate situation attracts the eyes of various government agencies and the mysterious transfer student Chiaki Kurihara, all eager to see if the upcoming captain lives up to her father's reputation. If the crew of the Bentenmaru want to maintain their status, they will need to set sail into the vast expanse of space and once again become a name to be feared.

As Hanabi Natsuno returns home after six years in Tokyo, memories flood into her. As she prepares to start high school, she moves to Tachibanakan, the local dormitory for female students. Upon her arrival, Hanabi stumbles upon a bare naked beauty, and instantly falls head over heels for her. She also reencounters Konomi Fujiwara, her childhood friend who she barely remembers. Hanabi is introduced to the other residence of the dorm and quickly becomes the center of attention. As the girls instantly take to the newcomer and begin shooting for her affection—subtly or obtrusively—Hanabi realizes that it is certainly going to be an interesting school year.