Lately, someone has been trying to take Nanami's life. Overhearing a conversation between Anthy and her brother Touga, Nanami misunderstands that Touga is the one who is trying to kill her. After that, someone saves Nanami out of a danger and she falls in love with him, who turns out to be a young boy. Nanami asks him to be her boyfriend, but she does not seem to know the difference between a lover and a henchman.

Juri believes there are no miracles. In the past, she secretly loved someone, but she couldn't win the person's heart. She thinks if there were miracles, she could have achieved her love. One day, Juri talks with Utena, and she gets enraged by Utena's words that she believes in miracles for the destiny between her "prince" and herself. Juri challenges Utena to a duel and tells her to show that there are miracles by defeating Juri by a miracle.

Utena meets Anthy's brother, Akio. Akio has been engaged to Ohtori Kanae whose father is the chairman of the board of trustees of Ohtori Academy. Her father is deceased, so Akio is the acting chairman. Mikage Souji is a twelfth grader who organizes Mikage Seminar, aka the Black Rose Association. He is such a genius that he even writes papers for professors. The building of Mikage's office is called Nemuro Memorial Hall, where it is said that one hundred boys were buried alive long ago. Chida Mamiya has a right to become the Rose Bride. Mikage says he will do whatever it takes to make Mamiya the Rose Bride, and will obtain the Power of Dios and the eternal secret. Mikage says the End of the World admitted Mikage and Mamiya. They say they need a duelist good enough to beat Utena. In the elevator of Nemuro Memorial Hall, Kanae confesses she is suffering. She can't get along with Anthy no matter how hard she tries. Taking advantage of that, Mikage makes her a Black Rose Duelist.

Tsuwabuki has still been serving Nanami as if he were her servant. Tsuwabuki's friend, Mari, isn't happy with him for being like that. She says Tsuwabuki is just being taken advantage of because he is just a child. Later, he begins to realize that he is treated as a child by Nanami. He wishes he were Nanami's age. Tsuwabuki asks Utena what he has to do to become a grown-up. Utena says it is probably to experience various things. Tsuwabuki tries to "experience various things" by watching kiss-scenes in films. Mari makes a fun of him, saying it is obvious that one who has experienced a real kiss is more grown up than one who has seen a hundred kiss-scenes. Tsuwabuki tries to do it with Mari and gets slapped. Nanami witnesses. When she asks him about the affair, Tsuwabuki realizes that he is treated as a child after all. At Nemuro Memorial Hall, he confesses that he wishes to grow up right now. Mikage takes advantage of him.

Mikage asks Utena to join his seminar again, actually trying to include her in his side, the Black Rose Association. This time, to convince her, he also offers himself as a consultant so that Utena can ask him when Utena or her friends have any problem. Thinking about Anthy's Rose Bride problem, Utena decides to see Mikage. But at Nemuro Memorial Hall, Utena finds photographs of Duelists, Kozue, Shiori, Wakaba, and others. Utena notices that Mikage is behind this whole thing. Utena challenges Mikage to a duel.

The End of the World use the recently injured Kozue to get Miki to duel with Utena! Of course, realizing it's his chance to get Anthy again.. he goes for it, and uses Kozue as his own Rose Bride!

Nanami finds out that her and Touga are not true siblings, and becomes overly depressed by this. To the point of running away from home... and suddenly being invited to live with Anthy and Utena by Akio! This is gonna more troublesome then a duel for Utena.