Utena Tenjou is a schoolgirl in the eighth grade of Ohtori Academy. She has the strange memory that, when she was very young, she met a mysterious "prince" and was given a ring with a rose signet. One day, Utena finds guys are making fun of a love letter somebody posted, and she finds it was written by her best friend, Wakaba, for the captain of Kendo Club, Saionji. For the sake of her best friend, Utena challenges Saionji to a duel. Then, Saionji tells her to come to the forest of the Duel Arena.

Winning the duel with Saionji, Utena is now the Victor of the Duel and is to be "engaged" to the Rose Bride, who is Anthy. Next day, Utena and Anthy start living together in a dorm. Saionji, who is actually really in love, asks Anthy to get back on good terms with him, but Anthy refuses. Then, he challenges Utena to a rematch. Feeling the whole thing is just crazy, Utena decides to lose the Duel on purpose.

In the tune Anthy just casually played, Miki found a "glow" that he had been seeking. He has a twin sister, Kozue, who used to play a tune with a "glow". However, she does not play the piano anymore because (he thinks) of his fault. Miki wishes to protect Anthy's "glow" in her tune; however Anthy tells him that, because she is the Rose Bride, by the Rose Signet Code, she must obey the Victor of the Duel, or Utena at the moment. She even says that, if Utena told her not to play the piano anymore, she would not. Since he thinks it is his own fault that he lost Kozue's "glow" in the past, not to lose a "glow" again, Miki challenges Utena to a duel and tries to set Anthy free and protect her with his own hands

Tsuwabuki heroicly rescues Nanami and ends up spending time in the infirmary. While he is recovering Utena and Anthy have an usual opportunity to read a secret diary he's been keeping on Nanami. But when Nanami's schemes are uncovered chaos arises and the bashful Tsuwabuki can't do anything to stop it.

An old friend named Ruka returns to the Academy after a long leave. He takes over the Fencing Team again, and then challenges Utena to a duel, using Shiori as a Rose Bride!

Anthy has Akio deliver some roses to a far away place, taking Utena with him. After a day at the Carnival, Utena and Akio bond late at night.

Touga suddenly comes back into Utena's life, wanting to spend more time with her. Then, Touga finally realizes the truth about his life.. and how much he was used.

Utena has gone though many battles.. Friends, Student Council, and people she barely knew. Nothing will compare though, to the battle she must fight now. Will she battle or will she not?

Everything comes to an end. Something shiny, eternity, miracles, the revolution of the world. Catch the stunning climax to Revolutionary Girl Utena!