In Tokyo, Pupulan plays a song on his flute to hypnotize children, following him into a mysterious ship before sailing off into the sky. Meanwhile, Serena, Rini, and the other girls bake cookies together at Lita's apartment. Serena ends up with cookies that look perfect and taste terrible; Rini produces the reverse. Rini sets out to give her cookies to Darien, but is stopped by a winged boy in strange white clothing standing outside the sweets shop. They befriend each other, and he causes some of the treats inside the shop window to dance by playing a tune on his flute before revealing himself as Perle. Meanwhile, Serena visits Darien with her cookies, and they argue over his friendship with Rini. They hear a report on the radio about the mass disappearance of children all over the world. Around the same time, Rini gives her bag of cookies to Perle before going their separate ways.
That night, Rini wakes up, and begins sleepwalking through the city. Diana wakes Serena, who along with the other girls, follow Rini and the other children. They save Rini, but get into a fight with Pupulan, and his "Bonbon Babies." Pupulan then hypnotizes the girls into seeing a Gingerbread House. In turn, Tuxedo Mask appears, and snaps the girls out of the spell. Queen Badiyanu orders her henchman Pupulan and the fairies to hurry up. Perle says outright that he does not believe in her anymore, but she seems unconcerned and orders that Sailor Mini Moon be captured. The ship lands, along with two others, in Marzipan Castle. When the doors are opened, the children run out into the darkness, except for Mini Moon. Looking into the shadows, she witnesses "Dream Boxes," each containing a sleeping child. Badiyanu lifts her into the air, commenting on the power she senses from Mini Moon, and explains her purpose. In the castle's center, a Black Dream Hole is forming, gathering the "sugar energy" of the sleeping children. Eventually it will overtake Earth, and all humans will enter into Dream Coffins.
Meanwhile, Perle leads the other Sailor Soldiers to a flying ship of his own. He tells them that Badiyanu promised that the children would be happy and safe in her world of dreams and where they can remain children indefinitely, but he thinks also of Rini, his friend. As they reach the castle, they are attacked, and after crash-landing fight Pupulan and the other fairies as well as three sets of Bonbon Babies. Just when the situation seems hopeless, the Scouts are saved by Sailors Neptune, Uranus, and Pluto. With this advantage, they are able to break the flutes of the three fairies, changing them into small birds. The Senshi infiltrate the castle and confront Queen Badiyanu, who has drained enough dream energy from the children, including Rini, to create the Black Dream Hole. The power drain is enough to force all the Sailor Soldiers except Super Sailor Moon into a half-detransformation. Taking Rini with her, Badiyanu enters the hole itself, and Super Sailor Moon follows. Sailor Moon then finds herself in Mamoru's apartment, carrying Rini. Darien lays her on the bed, then wraps his arms around Super Sailor Moon and tells her not to worry about anything, just to stay there with him. She asks him again who is more important, herself or Rini; he eventually tells her that she is. Super Sailor Moon lifts Rini in her arms once again, and eventually realizes that this experience is a dream.
As Sailor Moon tries to flee, Badiyanu demands Sailor Moon to give back Rini, but Sailor Moon refuses. Badiyanu assimilates herself into the black dream hole and attacks Sailor Moon. Hearing her mental cry, the other Scouts send their power to Super Sailor Moon, awakening Super Sailor Mini Moon. Together, they destroy Badiyanu using a double Moon Gorgeous Meditation attack. After the battle, Marzipan Castle is destroyed, and with Perle's help, the Senshi escape. The airships, each carrying children, return to Earth.
Later, at a beach, Perle gives Rini his glass flute, telling her that he is the fairy who protects children, and will always be with her. As Perle flies away, the Sailor Scouts watch the sun rise.