Set in an alternate version of the Meiji Era, a boy named Sakamoto Ryunosuke returns to Kyoto from Shanghai with his monster (youkai) Nekomaru. The law states that in order to live freely with humans, a youkai must be liscensed. The Kidou Shinsengumi Co. Ltd. is responsible for the capture of unliscensed youkais but must fight with the Tsubamegumi, who resents the new law. It turns out that Ryunosuke is the son of the owner of the Shinsengumis.

Set in the Meiji era, Kidou Shinsengumi Moeyo Ken tells the story of Kondou Yuuko, Hijikata Toshie and Okita Kaoru. These three are the daughters of former Shinsengumi members and, in the same fashion as their fathers were, they get called upon to protect Japan from its current problems. Much of their work deals with vanquishing the mysterious paranormal phenomena springing up ever more frequently in the Kyoto area and defending the city from any other dangers that may arise.

Ten years ago, the villainous scientist Dr. Hell led his wicked followers, known as the Underground Empire, in a struggle to destroy all of humanity. It was against these forces that the young hero Kouji Kabuto fought, piloting the legendary super robot "Mazinger Z." Kouji's victory stopped Dr. Hell's evil plan and returned peace to the Earth. Now Kouji has left the pilot seat behind and become a scientist in his own right, following in his father's and grandfather's footsteps. Yet an unexpected encounter deep under Mt. Fuji triggers an even greater threat to mankind than ever before and alters Kouji's destiny forever. With humanity's fate in their hands, Kouji and Mazinger Z face a choice between good... and evil.

Takumi Tsuzuki is a high school student who attends the Umenomori Private Academy, free of charge, alongside Fumino Serizawa, a childhood friend of his whom always says the opposite of what she feels. He spends most of his time at school fending off Chise Umenomori, the granddaughter of the board chairman and a pampered princess, who is constantly roping him into her eccentric hobbies. After school, he goes to work at the "Stray Cats" confectionery, a cake shop run by his adoptive older sister, Otome Tsuzuki, until it's time to go to bed. This is the average routine in the day and the life of Takumi. Mayoi Neko Overrun follows another seemingly average day in the life of Takumi. With his sister away from the shop, having gone to save someone else in need of help, Fumino takes it upon herself to wake him up so that he won't be late for their usual walk to school together, giving him a glimpse of her blue and white striped panties in the process. What a nice way to start the day. When Otome returns home, she brings with her a girl named Nozomi Kiriya, whose hair and mannerisms resemble that of a large cat. It turns out that she is a runaway that Otome can't help but take in. Takumi's ordinary days are transformed into splendid chaos as he tries to unravel who this mysterious beauty is and what she's running away from...