Jun Sakurada is a hikikomori, or a boy who has decided to isolate himself from the outside world, and legally does not go to school. In his time, Jun orders unorthodox items online, only to return them for a refund. One day, he receives a paper, asking whether or not to wind. After Jun carelessly accepts, a mysterious box appears with a doll inside. This doll, being able to move and talk, introduces herself as Shinku, the fifth doll of the Rozen Maiden. Jun enters a contract with Shinku, becoming her medium.

Hinaichigo, the sixth doll of the Rozen Maiden, and her medium, Tomoe, are introduced. Hinaichigo is always sad that Tomoe never has time to play with her. However, Hinaichigo does not realize that Tomoe has been gradually becoming weak due to their contract with each other. Shinku goes through a portal to the world of Hinaichigo, where the dolls must fight each other in the Alice Game.

Hinaichigo now lives with Jun and Nori, becoming Shinku's servant due to her loss in the Alice Game. Jun and Nori try to figure out what "unyuu" is, which is what Hinaichigo calls her favorite food. Meanwhile, Suigintou, the first doll of the Rozen Maidens, appears, encountering Shinku and Hinaichigo.

Suiseiseki, the third doll of the Rozen Maidens, is introduced from a flying box that crashes through a window into Jun's room. She takes everyone to Jun's dream world, which is actually a lifeless domain filled with memories of Jun's past. The doll also shows them how everyone has a soul tree that grows inside them.

Hinaichigo and Jun must battle Suiseiseki and Shinku to get to the truth of who took Hinaichigo's strawberry from her strawberry cake.

Suigintou takes Hinaichigo hostage. Jun, Shinku, and Suiseiseki enter the world of Suigintou and save Hinaichigo from the clutches of Suigintou. It is also shown that Jun is capable of bringing a clown doll back to life by sewing its broken pieces. Shinku suddenly collapses at the end of the episode due to exhaustion.

In order to save Shinku, and later Hinaichigo, from exhaustion, Jun must confront his fears of his middle school and retrieve a book containing information on the Rozen Maiden dolls that he discovers to be there.

Souseiseki, the fourth doll of the Rozen Maiden, is introduced. She lives with an old man, named Motoharu, who believes her to be his late son, Kazuki, which forces her to stay with him. Suiseiseki is traumatized by her twin sister's resolve to choose the Motoharu over her. Moreover, Suigintou soon intervenes.

Motoharu's past is revealed. Suigintou takes control of Motoharu's dream world and entraps Jun and the dolls inside it. Suigintou also takes Souseiseki's artificial spirit, Lempika. She then pressures Suiseiseki to hand over her artificial spirit, Sui Dream, lest Jun's life be endangered.

Suigintou wagers a battle with Shinku for the victor's Rosa Mystica at midnight.

The battle begins between Suigintou and Shinku. Suigintou seals Jun into his dream world where he begins to have a breakdown due to his past memories.

Jun recovers Shinku's arm and fixes it, something only Rozen was thought to be able to do. A final attack by Suigintou gets reflected by Jun, burning Suigintou in the process