The mutinous Musashi has been defeated, and the girls from Yokosuka Girls' Marine High School are safely back home. However, the Harekaze sustained critical damage during its final encounter with the Musashi and may not be able to sail again. Moreover, rumors spread that the Harekaze-class will be dissolved due to it lacking a ship. Other classes' attempts to scout members from the Harekaze's crew only make the situation even more uncertain. The answer to this dire problem may be found in the sealed orders that the secretary of the Harekaze, Kouko Nosa, is to deliver to its crewmembers. But time is running short...

Masahiro Setagawa is a hopeless teenager who is often used by the neighborhood bullies as an errand boy. Defenseless, Masahiro knows that nobody will ever save him. However, his life drastically changes when he meets Kousuke Ooshiba, a man known as the "Bear Killer," who takes down neighborhood gangs. A year later, Masahiro and his former friend, Kensuke Ooshiba, attend high school, only to find that Kousuke is their math teacher. While the three grow closer, Masahiro starts to view Kousuke as his "hero," and Kousuke develops an urging desire to protect Masahiro. However, their normal lives take a turn when Kensuke's childhood friend, Asaya Hasekura, returns, seeing Kensuke as more than just a friend, much to his surprise. Will the three boys be able to live a regular high school life? Or will forbidden love keep them apart forever?

Umaru Doma is a model student who has a hidden side: when she gets home each day, she puts on her hamster hoodie and turns into a sluggish otaku fond of junk food. As Umaru continues these daily antics, the friendship between her and her classmates—Nana Ebina, Kirie Motoba, and Sylphinford Tachibana—deepens, and more and more interesting events begin to unfold. Of course, these events give rise to numerous questions. What did Nana ask of Umaru's brother Taihei? Who is the mysterious girl with the diamond hairpin? And most important of all: why does this girl seem to know Umaru? These questions and more will be answered in Himouto! Umaru-chan R!

Ittoki Sakuraba fails to understand why his mother, his uncle, and his childhood friend, Kousetsu, seem to take his security so seriously. Kousetsu constantly follows and observes him with no regard for his privacy, focusing only on keeping him safe every waking moment. But the consistent hounding starts making sense when an adorable second-year student at his high school, Satomi Tsubaki, asks Ittoki out on a date. Though initially innocent, Tsubaki's true intentions soon become apparent when Ittoki visits her house; she plans to assassinate him, and she is not alone. Surprisingly, the ones who come to his aid are his uncle and Kousetsu—donning their dark and deadly ninja attire. After Ittoki is escorted to safety, his mother reveals the truth: he is the 19th heir to a noble clan of ninjas known as the Iga, and the target of assassination by their rival clan, the Koga. In order to protect himself against this new threat, Ittoki must hone his skills at the only ninja academy remaining in Japan: the Kokuten Ninja Academy.