Nagisa Aoi transfers to St. Miator Girl's Academy and gets acquainted with the school and fellow students, including Tamao Suzumi, her friendly (if somewhat overbearing) roommate, Miyuki Rokujou, the Miator student council president, and Shizuma Hanazono, the Etoile, whom Nagisa finds beautiful and intriguing but also frustrating and perplexing due to her forwardness in her advances.

Tamao invites Nagisa to the Literature Club where she recites a poem she wrote about a rainbow. Shizuma misses an important lunch discussion. Nagisa and Shizuma have a couple chance encounters; Nagisa runs into Shizuma in a hallway where Shizuma flirts with and attempts to kiss her before being interrupted by the toll of a bell, and Nagisa later finds Shizuma with a young Miator student. After the latter event, Nagisa retreats to the library, and Shizuma follows, catching her and again attempting to kiss her before being interrupted. The Miator student council president scolds Shizuma for her behavior toward the new transfer student and for shirking her responsibilities as Etoile, but Shizuma brushes it off.

Nagisa is shown around the Strawberry Dorms by Tamao and two of their classmates, during which time Nagisa is surprised by Shizuma yet again, who continues to make advances; Nagisa realizes that she finds herself unable to move whenever Shizuma gazes at her. Shizuma retreats to avoid members of the student council. Later, Nagisa accidentally bursts into a student council presidents’ meeting in the midst of an argument over the Etoile’s continued absence. Lulim's student council president, Chikaru Minamoto, tells Nagisa that her interruption was a relief because it ended the argument regarding Shizuma’s absence early. She explains some responsibilities of the Etoile that Shizuma is shirking as well as some major differences between the three schools, explaining arguments between the other student council presidents.

Hikari recalls being transferred to Spica a year prior and the first time she saw Amane riding her horse, thinking she was like an angel. Hikari and Yaya, her friend and roommate, sing in the St. Spica choir and practice for the congratulatory ceremony for the return of Amane and the rest of the horseback-riding team. Hikari, who is extremely nervous for the event, prays alone at a fountain for a good performance. She and other Spica students gather to see Amane’s return, at which time the Etoile presents Amane with a bouquet of roses for her accomplishments. At the ceremony, during the choir performance, Hikari accidentally starts singing early due to her nervousness, and becomes embarrassed. Amane stands to quiet the room and the performance progresses without Hikari’s participation; she is extremely disappointed in herself.

Select first years attending Miator become room-temps for older students. One such student, Chiyo, becomes the room-temp for Nagisa and Tamao.

Nagisa tries to find a club she would like to join, but she's not interested in any of them. Later, she discovers the Etoile's private greenhouse and helps with the flowers.

As Hikari and Amane's relationship progresses, Shion tries to convince Amane to run for the position of Etoile in the next election. However, unknown to Shion, Kaname and Momomi work out a different plan involving Hikari.

The "Seven Mysteries" of the Strawberry Dorms are mentioned. Nagisa and Tamao start to investigate the first mystery: "The Girl of the Hallway", despite Nagisa's terrible fear of the supernatural.

Nagisa starts to prepare for the mid-year exams by getting tutored by Shizuma in French.

Nagisa, accompanied by most of her friends, go on a short trip to the beach during "summer school". While there, everyone finds their own ways of having fun with each other, and they even get to participate in a test of courage later on. Meanwhile, Nagisa is just starting to discover just how much she misses Shizuma.

The month-long summer holidays have started, and most of the students residing in the Strawberry Dorms are going home. This leaves Nagisa, Shizuma and a couple of others left behind. Without the interference of other students, Shizuma makes her move on Nagisa.

Hikari finally gets a chance to be on a "date" with Amane. However, Kaname and Momomi again try to tear apart the new bond between them for Spica's sake at the Etoile position. In the midsts of all this, Yaya's feelings for Hikari grow even stronger, and she eventually vents them by suddenly kissing a shocked Hikari.

Yaya's incident with Hikari causes her to fear that she has lost Hikari forever. An effort by Nagisa and Tamao allows them a reconciliation and another chance at being best friends forever.

Everybody at the Strawberry Dorms is pitching in for the two plays in Astraea's Drama Festival. The main play, Carmen, is the focus of everyone's attention as everyone awaits the announcement of who is to be cast as the lead roles. The second play will be Romeo and Juliet, prompting a furious rock-paper-scissors and thumb war tournament between the second-years for the role of Romeo. Tamao is asked to write the script for the performance of Carmen.

While everyone is still preparing for the show, there seems to be some internal struggling concerning Kaname and Momomi with the others. Later, after suffering two show-stopping events, all the students involved with the play band together and put on a show the other students will never forget.

While all three schools eagerly await the election of a new Etoile couple, Nagisa learns the truth behind this tradition and receives an unexpected invitation from Shizuma in order to find out more information about Shizuma's late partner—the deceased Etoile.

During a rainy night in Shizuma's villa, Nagisa finally learns about Kaori Sakuragi, the Etoile that died. However, she also makes a painful discovery of exactly how close the two Etoile were, and how their shared past is still far from being a mere memory.

Miyuki recounts for Nagisa the events of the past few years concerning Shizuma and the now-deceased Kaori, whom they have both grieved for the past 3 years. As she tells her story, she also touches on the effects Nagisa's coming and passing had on both Shizuma and herself.

In the aftermath of Shizuma avoiding everyone else, a cheerful Nagisa pushes on with her life, but then falls into a state of depression and ponders if coming to Miator was a good idea, which causes Tamao to recount just why Nagisa is so important to her. Meanwhile, Nagisa's first and second year friends, concerned with her mood, decide to band together to cheer her up again. Tamao tells Nagisa of how she was lonely in her dorm room before Nagisa came, Tamao then opens the door and the others come in bringing cookies. The episode ends with Tamao talking to a sleeping Nagisa, and confessing her love to her before kissing her.

With the end of Shizuma's tenure as Etoile approaching, she prepares to abdicate her office. A final message from Kaori forces her to reconsider her life's choices, as well as her behaviour towards other people.

Preparations for the Etoile election are proceeding along and consuming more of everyone's attention. After another physical confrontation with Kaname, Hikari says something to her which motivates Kaname to challenge Amane to a game of tennis. During their match, Yaya and Hikari finally have an important discussion. During the match, Kaname admits that she both hates and loves Amane, because of her inability to ever surpass her at anything. Kaname's lover, Momomi, overhears this and after the match they break up. Amane becomes persuaded to join the Etoile election, with Hikari as her partner. It is also revealed that Tamao and Nagisa had been chosen to represent Miator in the Etoile election.

To counter Amane's plans of attending the Etoile election, Miyuki makes Tamao and Nagisa an offer not to be refused: enter the game together and repeat Miator's victorious history. Both Nagisa and Shizuma end up in an internal conflict as about how they truly feel, and tragedy strikes when Amane falls off her horse just as she is about to tell Hikari about her feelings.

Amane awakens after her accident, but has suffered partial memory loss—and among the lost memories is her relationship with Hikari, which leaves Hikari heartbroken. In the meantime, Nagisa and Tamao enter training for the Etoile Election and get an unexpected tutor: Shizuma.

Nagisa and Tamao continue practicing for the dance in preparation of the Etoile Election, but it will take some more of Shizuma's help to improve Nagisa's chances of becoming one of the next Etoiles. Meanwhile, Amane recovers her memories when Hikari sings the song she sang when they first met, and their relationship is consummated.

The Etoile elections have started. Shizuma makes her final decision about her relationship with Nagisa when she tells Nagisa she loves her in the middle of the ceremony, and the two end up 'eloping' just before the announcement of who won the election. While Amane and Hikari go forward together as the new Etoiles, Shizuma and Nagisa finally consummate their love, but Nagisa has to make up with the heartbroken Tamao.