Sei takes Yumi to visit Sachiko's house on New Year's Day where the Yamayuri Council have a party. All the major characters are reintroduced, and with the start of the New Year, Yumi looks happily forward to spring.

A series of photographs implicate Eriko in enjo kosai, or compensated dating, while Eriko's behavior becomes even more erratic and strange than usual. As it turns out, Eriko does have a secret, but its far from what she has been accused of.

In their midst of their graduation preparations for the third-years, the en boutons forget to organize a farewell party for the Rosas. To make it worst, Yumi finds out at the last moment that the en bouton petite soeurs must also put on a performance, and collapses from the pressure of all her various duties.

In the days before graduation, Rosa Chinesis and Rosa Foetida leave their parting words to their petite soeurs and grande-soeurs. Yumi begins to worry why Rosa Gigantea hasn't done the same. She swears to Sei she'd look after Shimako and promises to do anything as her final request, and Sei's answer leads to a surprisingly sweet moment and a revelation about her future.

Graduation day arrives. As the rest of the Yamayuri Council struggle with conflicting emotions, the Rosas reflect on their lives and the memories which shaped them.

With graduation's onset, Sei and Shimako remember the events which led them to become soeurs in spite of their many complex obstacles and reservations. The two of them ultimately form a deep and healthy relationship without becoming codependent.

Shimako falls into a depression after Sei graduates and cannot bear the weight of her secret alone. But a chance meeting with the down-to-earth Nijo Noriko gives her a new friend.

Shimako and Noriko become even closer, but a shocking revelation about Shimako's true religion is announced in front of the entire school, testing their relationship. Meanwhile, the Yamayuri Council is concerned over the state of Shimako's well-being and decide to take matters into their own hands.

Shimako is pressured to take Noriko as her petite soeur, but is hesitant due to the differences between Noriko and the general culture of Lillian. Caught between her loyalty to the Yamayuri Council and her desire to protect Noriko, Shimako quietly suffers until an argument forces Noriko into action.

Yoshino takes advantage of her newfound health by joining Rei's kendo club, causing extreme worry on Rei's part and another roadblock in their relationship.

Yumi and Sachiko have not been spending much time with each other, for Sachiko is always with Tōko. Every time Sachiko and Yumi are alone together, Tōko appears. Yumi begins to believe that Sachiko prefers Tōko over her.

Yumi gets back onto her feet with different people helping her out. She learns that she must develop an identity outside of being Sachiko's petite soeur.

Yumi learns why Sachiko has been so distant lately. With newfound confidence, she promises never to question Sachiko's love for her again.

Sachiko takes Yumi for a holiday in her summer home. While there, Sachiko's acquaintances make trouble for them.

Lillian and Hanandera collaborate on a school festival, and Yumi tries to fix Sachiko's hatred for men.

Hosokawa Kanako, a first year, sees Yumi as the ultimate embodiment of perfection. When preparations for the Hanadera Festival begins, Kanako tries to keep Yumi away from it due to her hatred of men and her fear of having Yumi be corrupted.

Lillian's School Athletic Festival begins, and Kanako and Yumi make a bet to settle the problems which began between them last episode.

The second year students go for a week's study-vacation in Italy. Yumi meets up with Shizuka Kanina while there.

Yumi and the Yamayurikai prepare a production (The Tale of Torikaebaya) for the upcoming school festival with neighboring boys school, Hanadera.

The day of the School Festival has arrived, there are many attractions but most importantly, the drama club is performing Little Women and Yamayurikai, The Tale of Torikaeba. With so much going on, the day might not just be another ordinary day.

This year's remaining, petite soeur-less en boutons, Yoshino and Yumi are feeling the pressure to find their little sisters, for various reasons. Yoshino suggests that they have a Soeur Audition to do just the thing.

The day of the Soeur Audition—turned into Tea Party—arrives, and soon the Kendo Competition, as well. Yoshino has been looking forward to the Kendo competition, but she has promised Eriko that she will have a petite soeur by then. Someone catches Yoshino's eye, but it looks like it might be more complicated than it seems.

Yumi and Sachiko finally go on their date to the amusement park. However, Kashiwagi and Yuuki turn up, with Kashiwagi bearing a certain agenda in mind. Yumi learns a few things and Kashiwagi's intentions are made clear.

Tōko suddenly shows up on Yumi's doorstep in a strange situation and ends up being over for dinner, while Suguru and Yumi have an agreement. As well, Rei and Sachiko have an understanding.

The Yamayurikai Christmas party takes place. Tōko and Kanako are both invited to the party, but afterwards, Tōko rejects Yumi's offer of the rosary, and Yumi is crushed.

Yumi and the rest of the Yamayurikai are invited for a female-only new year party, where Yumi has an interesting dream that could be applied to her current situation.

With the elections for the next year's Student Council approaching, Tōko unexpectedly enters the race with murky intentions.

Sachiko and Suguru Kashiwagi discuss Tōko's entry in the Student Council elections and her recent behavior towards Yumi. The Lillian Newspaper Club organizes another card hunt event for Valentine's Day, while Noriko worries that Yumi has given up on Tōko. As well, the Gigantea soeurs have a small discussion about the 'next Rose'.

As different people in her life try to help her find happiness, Tōko continues to run away from their support. Suguru warns Tōko that if she continues to run away, one day no one will chase after her. More details of Tōko's family situation and her reason for refusing to be Yumi's petite soeur are revealed.

After Tōko realizes her large misunderstanding, crying, she is comforted by Noriko. The next week, the Valentines' Day Card Hunt for the Next Roses take place with surprising results. Sachiko and Tōko have an interesting conversation on the stairs, and eventually Tōko comes to realize something vital to her relationship with Yumi.

The Valentines' Day dates take place, with Chisato Tanuma finding Yoshino's card and Tōko finding Yumi's. During Tōko and Yumi's date, even more about Tōko's past is revealed, as well as her reasons for running away from home. They eventually visit the hospital owned by Tōko's grandfather, and Touko slowly starts to open up to Yumi. The season ends with Yumi's thought of Tōko accepting her rosary.