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.

Third-year high school student Jirou Yakuin is in love with his childhood friend and classmate, Shiori Sakurazaka. Thus, he hopes to be paired with her for the "marriage practical": their school's practice of randomly selecting boy-girl pairs to live as pretend married couples while monitoring and rating them on how close they have gotten. Meanwhile, the lively Akari Watanabe wants to be assigned to her crush, the popular and good-looking Minami Tenjin. Much to their dismay, Jirou and Akari find out that not only have they been paired together, but so have Shiori and Minami! Determined to be with their crushes, Jirou and Akari strive to earn as many points as possible, as the top 10 pairs earn the right to switch their partners—so long as both couples agree.

What do an alien, former ninja, weak telepath, and boy pretending to be a girl have in common? They are all classmates at Kashihara Girls' Academy, and they hide their true identities from the world. Rikka, Chiyo, Sekine, and Tsubasa seem like the best of friends, but they each harbor a monumental secret that they cannot reveal, no matter what. In order to continue masquerading as normal middle school girls, each of them must invent creative ways to conceal their true selves. But that is easier said than done, as the four students end up entangled in numerous shenanigans along the way.