During the events of the original Rozen Maiden, after circling yes on a paper and agreeing to wind an unknown something, a traumatized Jun Sakurada fights alongside the lifelike dolls known as the Rozen Maidens. But what would have happened if Jun had circled no? Jun, having gotten over his school trauma from his younger days, spends his time attending college and working in a bookstore. However, he does not feel as though he belongs anywhere. One day, he finds a book containing instructions on how to make a Rozen Maiden. Mysteriously, when he arrives home that night, the second volume in the book series has been delivered to his house, along with some pieces of a doll. But as suddenly as they started arriving, the books stop coming, and Jun gets a notice that says that the books have ceased being published. With an incomplete doll in hand, and a message from his other self in another world, this Jun also finds his way into the world of the Rozen Maidens.

It has been one year since Tsukune Aono enrolled at Youkai Academy, and since then his life has taken an interesting turn. In addition to being the only human at a school for monsters, he has attracted a bevy of beautiful women who want him all for themselves: the sexy succubus Kurumu Kurono; Yukari Sendou, a witch; stalker and yuki-onna Mizore Shirayuki; and Moka Akashiya, a kind vampire who, when her rosary is removed, reveals a darker personality. But soon, trouble visits Youkai Academy in the form of Moka's younger sister, Kokoa Shuzen. She is furious that her true older sister is sealed within Moka's rosary, and vows to bring out Moka's darker self. However, Kokoa's thoughtless actions may affect more than just her sister...

The adventure of Hepoi, a hero of heporis, Ryuuto, the prince of Dragonia, Miiya Miiya a fairy looks like a cat, and Bunzaemon, a merchant, to defeat Dracunes, the King of dark side castles.

As Jun Sakurada fights and lives alongside the Rozen Maidens, special lifelike dolls made to battle each other, he enjoys a rare break in which he is told a story during the events of Rozen Maiden: Träumend. When Jun buys a brooch as a present for Shinku, the fifth doll, she refuses to accept it at any cost. Souseiseki, the fourth doll, then recounts the story of how Shinku and the first doll, Suigintou, first met. This tale tells of the cruel and heartbreaking circumstances surrounding Suigintou's birth, and how the many misunderstandings between her and Shinku shaped their longstanding rivalry fueled by Suigintou's unfettered hate towards Shinku. The stage is set in Rozen Maiden: Ouvertüre in 19th century London as the story delves into the past of these one-time friends and the secrets that they hold.