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

Jun has overcome his past and must now make up all his schoolwork before he can actually go back. Suiseiseki and Souseiseki barge into the Sakurada residence as usual, the dolls play with each other, and everything is back to normal. However, Shinku starts to face deep nightmares about Suigintou. Barasuishou, the fraud of the seventh doll of the Rozen Maiden, is introduced.

Shinku claims that Barasuishou never meet any of the dolls of the Rozen Maiden. Since Barasuishou is the seventh doll, this appears to be a sign that the Alice Game would be ending soon. Shinku's strange behavior continues, and Jun continues to worry about her. Jun and Tomoe also visit the doll shop of a doll maker named Enju.

Kanaria, the second doll of the Rozen Maiden, is introduced. Her initial plan is to sneak into the Sakurada residence and take the Rosa Mysticae from Shinku, Hinaichigo, Suiseiseki, and Souseiseki. However, chaos erupts as the dolls think that a burglar broke in.

Suiseiseki decides to find a medium, as Jun is the only one eligible, though she is skeptical about him. Ultimately, Jun and the five dolls are taken to the world of Barasuishou, where the Alice Game is foreshadowed. Jun enters into a contract with Suiseiseki.

Hinaichigo tries to send a letter to Jun. Suiseiseki tries to earn Jun's respect. Souseiseki tries to keep order in the house Kanaria tries to get into the Sakurada residence yet again. Jun and Shinku are in the background during these events.

Megu, hospitalized with an incurable disease, enters into a contract with Suigintou. However, Megu wishes only for death and insists that she is incomplete and broken. After encountering Barasuishou, and later Shinku, it is realized that Suigintou was revived to participate in the Alice Game.

Kanaria makes her resolve to fight, in order to both remain alive and to make her medium, Micchan, happy. However, conflicts get resolved and Kanaria fulfills Micchan's wish a different way. Meanwhile, Souseiseki starts to see deeper into the Alice Game and begins to believe that she and her sisters should fight.

After having seen an apparition of Rozen, the creator of the dolls of the Rozen Maiden, Souseiseki soon sees the deep meaning behind the Alice Game. After having seen Enju and his feelings about dolls, Jun starts to wonder more about Rozen and his love for his dolls. Souseiseki resolves to fight her sisters, take their Rosa Mysticae, and become Alice.

Suiseiseki becomes worried about Souseiseki. Souseiseki battles against Barasuishou and Suigintou, only to be defeated. Souseiseki asks Suiseiseki to take her Rosa Mystica, but Suiseiseki fails and Suigintou takes Souseiseki's Rosa Mystica.

Souseiseki is destined to meet a tragic fate, and to make matters worse, Shinku sees the same for Hinaichigo as well. Hinaichigo is also aware of her destiny, and shares her last moments with Tomoe. There is no time to mourn, however, since Barasuishou, Laplace, and Enju have apparently laid a trap for Jun and the remaining dolls of the Rozen Maiden.

Because they have yet to fulfill Rozen's wish, the remaining dolls fight Barasuishou and Suigintou. When things spiral downward, Shinku is left to fight Barasuishou.

The conflicts are solved, the battles are ended. Jun learns the shocking truth about Barasuishou, Enju, and Rozen.