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.

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.

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.

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.

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

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.

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.

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

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.

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.

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 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.

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

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.