It's the first day of school at Ohtori Academy and already Tenjou Utena, 8th grade, is being yelled at for wearing a boys uniform to school again this year. Her best friend Shinohara Wakaba massively glomps (a big tackle like hug, usually from the back) Utena for ditching her in the morning before class. After regaining her balance she notices a disturbing scene outside. A green haired man is hitting a young purple haired woman. Wakaba tells Utena that the green haired guy is Saionji Kyouichi, the vice-president of the student council. The purple haired girl is Himemiya Anthy. Anthy is a very quiet and reserved person. Most people stay away from her. As Saionji is about to slap Anthy again, Kiryuu Touga, the President of the student council, stops him. At a student council meeting, the members are discussing how Saionji is treating Anthy. Everyone refers to her as the Rose Bride. Kaoru Miki says that the everyone who wears a rose seal is a student council member. Kiryuu Touga says that the student council exists by the will of 'The Ends Of The World'. Saionji says that if Touga doesn't like how Saionji is treating the Rose Bride, he can follow the rules of the Rose Seal and duel for possession of the Bride. Touga mentions that a new duelist will arrive soon to challenge Saionji. Utena and Wakaba are sitting on the grass when Wakaba asks Utena about her ring. Utena says that all she remembers is that a prince gave it to her when she was very young. A commotion draws Utena and Wakaba to a message board where someone has put up someone else's love letter. It turns out to be a letter Wakaba wrote to Saionji. Utena, furious at the way Saionji has embarrassed her friend, challenges him to a duel. Saionji is about to refuse when he sees a ring on her finger. A ring with a rose engraved on the top. He realizes she must be the new duelist and tells her to meet him in the dueling forest in the evening. 'The forest no one is allowed to go into'? Utena arrives and sees that there is a massive locked door. She grasps the handle and a single drop of water splashes onto her ring. The door opens to reveal and enormous spiral staircase that wasn't visible outside of the forest. She ascends the stairs to the dueling arena where, to her shock, she sees Himemiya Anthy waiting with Saionji. She also sees a castle suspended upside down over the dueling arena. Anthy puts a rose on the breast pocket of Saionji and Utena's shirts and tells Utena if the rose is knocked off, she loses the duel. As is an upside down castle weren't enough, Saionji proceeds to pull a sword out of Anthy's chest! He calls it the sword of Dios. The duel begins and Utena is holding her own pretty well until her wooded practice sword shatters. There is a final lunge by both and then....Saionji's rose blows away in the wind while Utena's still remains in her pocket. As Utena is walking home, she sees Anthy standing in the road. Anthy says 'I have been waiting for you. I am the Rose Bride. From this day forward, I belong to you.'

It's another ordinary day at Ohtori Academy (if there is such a thing). Wakaba has gotten over the prank Saionji pulled and glomps Utena as usual. The student council members are in the elevator. As they ride, they recite: 'If it cannot hatch from it's shell, the chick will die without ever truly being born. We are the chick; the world is our egg. If we don't break the world's shell, we will die without truly being born. Smash the world's shell, for the Revolution of the World!' The council discusses the rules of the rose seal and the new duelist, Utena. Whoever is the champion of the duels and possesses Anthy will gain the right to enter the castle and gain the power to revolutionize the world. The student council gets letters from 'The Ends of the World' that tell them when a new duelist is coming, who has won/lost the duels, and who will duel next. Utena find out, to her surprise, she has been assigned a room in the south (haunted) dorms with Anthy. Anthy explains to Utena that as long as she is the current victor, others will come to challenge her to duels. Anthy however will not say anything more about the strange floating castle and the sword of Dios other than 'they are mysteries.' Utena thinks this is stupid and decides to just purposely lose to get out of the duels. Saionji arrives at Utena's dorm to challenge Utena to another duel. Utena accepts. Although she has 'decided' to lose the duel, when Saionji is about to cut off her rose, Utena protects it with her hand. Saionji tells her that although she is pretty good with the sword of Dios, it has no power of its own. Utena's ring flashes and the apparition of Dios himself descends from the castle and merges with Utena. Utena lunges at Saionji and cuts his rose from his chest. Later, Anthy asks Utena why, if she intended to lose, did she fight so hard to win. Utena says she did it for ChuChu who would have been teased if he and Anthy had gone back with Saionji.

Utena is walking with Anthy and telling her that she doesn't have to do all this 'miss Utena' stuff. As they pass the courtyard, Kiryuu Touga introduces himself as the president of the student council. He infers that maybe he is the prince she has been looking for. Touga has become interested in Utena since he saw her unleash the power of Dios for a second in the duel. His sister, Kiryuu Nanami, is incredibly jealous of both Utena and Anthy. When Touga invites Utena to a dance, Nanami invites Anthy and gives her a special dress. It turns out to be a dress that will dissolve in water and just when Utena is about to tell Touga about her prince, Nanami has someone spray Anthy with champagne which dissolves her dress. Utena runs to the rescue and with a flick of her hand, makes a dress for Anthy out of a tablecloth. Utena is soon challenged by the rest of the student council.

Utena meets Kaoru Miki because of Miki and Anthy's shared talent in playing the piano. When Miki was little, he and his sister Kozue would play the piano in the garden. What Miki didn't know was that Kozue wasn't very good at all but Miki was so good he could cover his sisters mistakes. After a ruined concert, Kozue refused to play ever again. Miki is searching for his 'shining thing' since then, and finds it in Anthy's piano playing. Miki knows that Anthy can't play freely, since she is engaged to Utena and can only play if Utena says so. To 'free' Anthy, he challenges Utena to a duel and loses. Utena and Miki stay good friends however. Anthy tells Miki that she would like to play with him.

As Nanami is walking along, it becomes apparent that someone is trying to kill her. Lately, there have been a series of potentially dangerous accidents around her. After hearing part of a conversation between her brother and Anthy, Nanami believes it is he that is trying to kill her. An elementary school kid named Tsuwabuki Mitsuru is really behind it all. He once saw Touga save Nanami from a runaway horse and decided that he wanted to be a 'big brother' to Nanami so he set up the 'accidents' so that he could rush in and save her. However, when a runaway kangaroo (?) goes after Nanami, Touga once again is the one to save the day. Nanami asks Tsuwabuki to go out with her but what she really has in mind is a servant more that a boyfriend. To be by her side however, Tsuwabuki is glad to accept the arrangement.

Arisugawa Juri is the next to challenge Utena. Long ago, loved someone in secret. She never told that person of her feelings and when that person went out with someone else, she realized she could never have that person. With the loss of her love, she lost her belief in miracles. If there truly were miracles, she would be able to have her love. Touga theorizes that Juri wants the rose bride and the power to revolutionize the world to get her love but Juri claims it is to disprove the power of miracles. As Utena and Juri fight, Juri knocks Utena's sword out of her hand and is able to cut the rose off her chest when Utena's sword falls from the sky and hits Juri's rose knocking it off of her chest first. Juri refuses to believe that a miracle has happened and leaves.

In cooking class, Utena and Anthy are making curry. There is a huge explosion and both Utena and Anthy are taken to the hospital. They are released soon, but something is strange. Utena still seams weak, and Anthy retaliates against Nanami's henchmen by slapping them. It becomes apparent that the explosion caused Utena and Anthy to switch! Under question, Nanami admits that she had someone switch the regular curry powder with 1 billion fold spice. Nanami is sent to India to get more so that Utena and Anthy can be switched back, and she drags her henchmen with her. Everywhere they turns, a herd of elephants seems bent on stopping them. Meanwhile, there is chaos as few actually know about the switch. Saionji approaches 'Anthy' (Utena) and takes her to a dark, secluded room. He tells her its time to do what they always do here and he starts to unbutton his shirt. 'Anthy' sweatdrops until Saionji reveals that he only wants her to write in their exchange diary. (a diary where they write their feelings of love for each other >.>) After seeing an entry from Saionji where he draws a very unflattering picture of Utena being pierced by his sword, she knows just what to write. Nanami finally returns but she slips on a banana peel left by Chuchu and all the 1 billion fold spice blows away. Fortunately, it turns out that the original can of 1 billion fold spice was never opened, thus it was Anthy's cooking itself that caused the switch. Saionji drops by for a dinner that is meant to switch Anthy and Utena back, demanding to know why 'Anthy' wrote 'dumbass' in the exchange diary. He and Chuchu eat some of the curry at the same time and Chuchu ends up practicing his kendo as Saionji climbs a tree and eats a banana.

Before anyone else has a chance to challenge Utena again, Saionji (returned to normal of course) receives a letter from The Ends of The World. He has been talking with Utena about how he refuses to lose to Touga. They were childhood friends and fought lots of duels. He wants to get to the castle to gain eternity. The letter he has received says the castle in the air is coming down. He takes this to mean his chance to enter the castle. At the same time, Utena gets a call that says Anthy has been kidnapped. Utena finds Saionji face down in a pool by the dueling arena. She revives him and both are shocked to see the gates to the dueling arena open since neither unlocked them. When they get to the top, they find Anthy unconscious and trapped in a rose shaped structure. Utena saves her and Saionji, ignoring the rules of the rose seal, tries to attack Utena to gain possession of the Rose Bride. Utena is saved at the last moment by Touga who takes the hit and is injured by Saionji's sword. Touga is mended, Utena and Anthy are safe. It turns out the letter was a fake and a trap and Saionji fell for it.

Saionji has been expelled for his violation of the rules and his injuring of Touga. Kiryuu Nanami feels that Utena is the cause of the injury to her brother, since he was hurt protecting her. She is reminded of a time when she gave a kitten to her brother as a birthday present. Touga liked the kitten so much, he started playing with it more than he payed attention to her. In jealousy, she got rid of the kitten. When Utena shows up at a party for her brother with flowers to thank him for saving her, and Anthy shows up with a kitten she found, Nanami almost loses it. She wants to get revenge on Utena, but the school has very strict rules about fighting. To solve the conflict, Nanami is made a duelist and she immediately challenges Utena to a duel. Utena cuts Nanami's rose off, but Nanami continues to attack Utena. Touga stops her and tells her there will be another time.

Finally, the time has come for Touga himself to challenge Utena. He convinces Utena that he is indeed the prince from her childhood. Utena, believing that Anthy wants to be a normal girl, accepts the challenge and knows she has to defeat her prince to save Anthy. Its not as easy as she thinks and during the duel, Touga lowers his sword and waits for Utena to destroy his rose. Utena can't do it and Touga defeats her and gains possession of the Rose Bride. Utena tells Touga that Anthy wants to be a normal girl and have friends. Touga explains that Anthy only said those things because as the Rose Bride she does what her master wants, thinks how her master wants her to think, and feels how her master wants her to feel. After Touga won the duel, Anthy says she likes being alone and likes being the Rose Bride following Touga's wishes. Utena is devastated.

The next day, Utena goes to class in a normal girls uniform and tries to forget about the duels, and Anthy. She tries to convince herself that it is better this way, to be a normal girl instead of a prince who saves others. 'I am normal now' she tells Wakaba. Wakaba tells her: 'for you, it is NOT normal' Wakaba's words hit home and she realizes she has to get herself, and Anthy back. In a way, you might say that Anthy has become a part of her. Touga asks Utena out to dinner and Utena responds with a duel challenge. During the duel, Touga shows Utena the real power of the sword of Dios. He calls Anthy over to protect the sword and it becomes infused with power and glows. The sword of Dios begins to cut through the sword Utena borrowed from Juri. Then, something spectacular happens. The Rose Bride, seeing Utena about to be defeated, is moved to tears! The Rose Bride is experiencing a strong emotion all her own which is completely opposite to her nature and yet the tears fall. As Anthy cries, the sword of Dios loses the power it gained in the beginning. With Touga shocked at what has impossibly happened, Utena defeats him and becomes the champion once again.

A strange man with purple hair is standing in the dueling arena. He looks up suddenly and grins. The castle falls to the arena floor. Inside is a young boy sitting on a ball of some sort. The man calls him 'Dios' The duels so far are reviewed and are listed: 1.friendship (amitie) 2.choice (choix) 3.reason (raison) 4.love (amour) 5.adoration (adoration) 6.conviction (conviction) 7.self (soi). The man tells Dios that Utena may be the one they have been looking for. The one who will reach the Duel named Revolution and release the power of Dios. Dios raises his head and the man reacts as though Dios was glaring at him. It seems Dios isn't so happy about what the man has said. The man assures him that day will be mutually beneficial...