Tenjou (above heaven) Utena is an orphan 13 year old who lives with her designer aunt. Her tomboyish ways and habit of dressing like a boy gets her in constant trouble with the teachers at her junior high school, but as she explains, she's always running and falling down and if she wore skirts the guys would get a lot of looks at her underwear.
Seven years ago, after her parents' death, she was walking in a daze by the side of a river and was accidentally pushed through a gap in the fence and fell in. But an unknown young man saved her. She can't remember his face, only the smell of roses that hung about him. He gave her a ring carved with a rose and told her that if she kept her high and noble spirit the two would definitely meet again. Every year when the roses bloom, Utena gets a card from this unknown young man, in an envelope with a rose seal, saying they'll meet again. This year the card says 'This year I'll definitely see you.' Her friend Kaidou, always the rationalist, tries to persuade her that the cards were sent by Utena's aunt in an attempt to cheer her up, but Utena begins to keep an eye out for her unknown prince.
She thinks she's found him in her aunt's young assistant Wakaouji (young prince) who comes to the house carrying roses and who wears a ring like Utena's own with the rose seal. Utena learns that the ring comes from his school, where it's given to elite students, and she's happy in the belief that she's found her prince-- until she and Kaidou find the aunt and the assistant kissing. Utena in shock runs out of the building and along the riverside to the very spot where she fell in as a six year old. And there's a little lost girl crying, who runs away from Utena's questions through the hole in the fence and slips down the embankment. Utena grabs her arm to pull her up to safety, but gets pulled in after her. Kaidou, watching from the other bank, sees her fall in- then sees across the river the little girl in her mother's arms and a dark-haired man holding Utena. The man has vanished by the time Kaidou reaches Utena's side, but he leaves the same scent of roses as came from Utena's letters. Kaidou shows Utena how the cards from the Prince form a picture when put together- the picture of Ohtori Academy, and Utena decides that that's where she'll meet her Prince.
Utena goes to Ohtori Academy. When she's been there six months, she sees for the first time the members of the School Council, an elite body that does pretty much what it pleases. Specifically, she sees the vice-president, Saionji, (green wavy hair) slapping his girlfriend Annecy (in the glasses) around until the president, Touga, (red hair, straight) stops him. There's a special meeting called, attended by the other members of the student council- Julie, the head of the fencing team, and Miki, a ninth grader who's a piano and fencing prodigy. Saionji defends his right to treat Annecy as she pleases- she's the Bride of the Rose and she belongs to him according to 'the Rules.' Annecy agrees with this- 'I belong to Saionji-sama. He can do what he likes with me.'
Meanwhile Utena's friend Wakaba has sent a love letter to Saionji which somehow gets pinned up on a public bulletin board for everyone to read. Utena has always said she wants to be a prince herself, not the princess who always has to be saved and protected. In good princely disgust she breaks in on Saionji at his kendou practice and challenges him to a duel. He says 'Fine- meet me at the duelling platform tonight.' The duelling platform lies behind locked gates which Utena's ring somehow opens, through a thick woods and up an immensely long staircase. At the top is an open space, with an upside down castle hanging above it. Saionji is quite casual about it: 'Must be some kind of mirage.' Annecy is waiting, in formal dress, to pin a rose to both Utena and Saionji's chest. The one who dislodges the rose has won the duel. Annecy calls on 'The sword of the Rose- the power of Dios which sleeps in my breast': and to Utena's surprise Saionji then draws a sword out of Annecy's chest. It's a real sword, too, that cuts Utena's bamboo blade in half- but Utena refuses to yield and knocks Saionji's rose off him. The sword of Dios flies up in the air and lands in Utena's hands, where it gives off a great flash. Touga has arrived just in time to see Utena win the duel. Cat that he is, he gives her a seductive smile as she goes and says 'I'm falling in love with you.'
Utena finds she has to leave her dorm and go to an old building where no one has lived for ten years. No reason given: she suspects reprisals for having beaten Saionji. The place is filthy, but her own room is spotless because Annecy, her new roommate, has done a thorough cleaning. "I'm the Bride of the rose," she explains smiling. "I'm engaged to whoever has the sword of Dios." Utena is less appalled at having a fiancee of her own than at Annecy's sweet acceptance of her status as trophy and chattel. But the two settle down to dorm life together, along with Annecy's little friend Chuchu, a kind of mouse-monkey. Annecy tells Utena that the ring she wears marks her as one who has the right to engage in the official duels- and that all the members of the Student Council will be waiting to challenge her. Utena storms off to the SC's special rose garden/ conservatory to have a word with Touga about all this. In the conservatory she thinks she sees her prince: but when she runs in, the prince turns out to be Touga. He tells her that the 'game' of duelling and winning the Bride of the Rose was decided by a mysterious figure called Sekai no Hate- the End of the World. The 'hero' who shows himself worthy of having the sword of Dios by winning the series of duels and the Bride of the Rose, will eventually reach the castle in the air and lay hands on power great enough to change the world. Through volumes two and three Utena does indeed take on the members of the Council, often quite unwillingly. Julie challenges her first, the motive being a concealed jealousy on Julie's part for the attention that Touga is showing Utena. Miki says he has no intention of fighting Utena- but his twin sister is captured and imprisoned in a glass coffin from which Touga says she'll never be released until Miki follows the rules and fights Utena. Suspicion that Touga is Sekai no Hate is increased by the discovery of an underground room in his house with a chart that shows all the past and future duels that will take place.
At last Utena gets another card from her prince, with a picture of the conservatory and the message 'At last we can meet.' She runs to the conservatory- and finds Touga there. He tells her he's the prince she's come to meet, and Utena is half-persuaded-- until Annecy comes in to water the roses and Touga tells Utena to ignore her. 'The Bride of the Rose has no heart. Her heart can never belong to another. She enjoys being what she is.' Utena has spent a lot of time getting to know Annecy and persuading her it's ok to have a mind of her own, and Touga's cold judgment revolts her. She drags Annecy away and starts getting her to associate with other girls.
That night Utena awakes to find Annecy gone, and sees her running happily away from the dorm. She follows her to a planetarium, and meets Annecy's brother Akio, (dark hair in a ponythail in the manga; silver ditto in the anime) the acting head of the school. Utena is a little wistful at the idea of having a wonderful older brother like Akio, but the reader may be forgiven for wondering about how Annecy feels about him.
Finally Touga challenges Utena to a duel. Utena protests against it, saying it's hard on Annecy always facing the possibility of having a new fiance at evry fight. Touga holds Utena in a close embrace and tells her there's no need for her to play at being a prince or to protect Annecy. 'I feel sorry for you, knowing nothing and thinking you need her.' Utena is confused by her conflicting feelings, and loses to Touga. Touga then tells her that he simply made use of Utena's emotions in order to beat her and get the power of Dios for himself. Utena is less upset at being betrayed than at seeing Annecy turn into Touga's sweetly smiling doll, who agrees with everything he says; and at being patronized by the macho Touga. ('Wanna go out with me next Sunday? Just the two of us?' (leer)) In depression she starts wearing girls' clothes, which sends her friend Wakaba into fits. 'It's not you! It's not like you! Go back to being yourself!' Thinking over Wakaba's words, Utena returns to her lonely dorm and finds a new boy's outfit waiting for her with a message from the prince. She puts on her uniform and challenges Touga to a second match, with an extra condition. If Touga wins, he promises to give up the Council. If Utena wins, she promises to become Touga's.
The duel is hard fought, but Utena wins through her sense of resolve: 'I don't care if I get hurt. I only care about keeping my pride and protecting Annecy.' At those words the strength of the sword of Dios that Touga is holding vanishes, and a ray of light from Utena's ring blinds him, and she succeeds in knocking the rose off his chest. The spirit of Dios descends from the castle for all to see, a confirmation that Utena holds the power of Dios. As promised, Touga resigns and declares his intention of following Utena-- so as to be near the power he longs for. This means he moves in with Utena and Annecy, which is a nuisance. But he also warns Utena that since she's the final winner of the duelling game, Sekai no Hate will soon try to get her for his own, since he too desires the power of Dios; and that Utena shouldn't trust Annecy. Utena confronts Annecy, who warns her about Sekai no Hate. 'If he can't get you, he'll try to destroy you. And if he can't do that, he'll take what's most precious from you!' And the next thing Utena knows, there's a fire at the dorm and she dashes in to save Wakaba and is nearly overcome by smoke- but Annecy's brother comes after her and jumps with her to safety. Very nice: but on the next page you discover Akio is Sekai no Hate himself.
Volume four concerns the Perils of Utena as she gets preyed on by Akio- a macho pig and manipulator who makes Touga look like an amateur. Utena does indeed fall for him. He gets her to carry out the betrothal ceremony with Annecy, which turns Utena herself into the Bride of the Rose and Akio into the Prince, who sets off for the castle overhead to get the power of Dios for himself. Dios has been shut up in the castle in a trance for countless years while Akio looked for a way to get to his power. Utena is quite calm about all this until she sees Annecy in her crystal coffin and hears Akio dismiss his sister- 'Her role is over. You'll be a much better Bride than she was. The two of us will rule the night together.' She rejects Akio who goes to get the power of Dios for himself alone. Utena mangaes to free Annecy, who tells her that Akio intends to kill Utena's prince as the only way to get his power. They go to the castle together while Annecy tells Utena a bit about their past. Annecy was fated to die but Dios rescued her, and thus became fated to take on the role and the power of the Prince. Annecy loved and respected him. Akio was Dios' friend and like a younger brother to him, but in time he became jealous of Dios' power and attacked him. Dios refused to hand over his power and shut himself up in the castle. A portion of his power became a sword and remained in the breast of Annecy who had loved him. 'It's like a myth' Utena tells her, and Annecy says, 'Yes, it's a myth.' But at that moment the castle begins to crumble. Utena runs to see what Akio has done. She finds Dios sitting asleep on a giant globe and thinks she's come in time- but he slips sideways and Utena sees the sword in his breast. Akio appears and says he killed Dios- but that Utena need not grieve. 'Your prince isn't dead. I am the one who was Dios.'
End volume 4, with one foot over the cliff.