The drama club is finally re-established and Koumura is shared with the choir club. Tomoya's home room teacher goes to Tomoya's house to ask his father about his future, but Tomoya's father says that is something that Tomoya has to decide for himself. Seeing the strained relationship between Tomoya and his father, Nagisa offers to have Tomoya stay over at her house for the time being, which he accepts. After coming home from school, Tomoya finds several small kids in Nagisa's house, and finds out Sanae is instructing them in a cram school. Nagisa confides to Tomoya that she feels she did something really bad to her parents in the past, but she cannot remember what it is, and her parents say that she must be imagining it.

It is now during summer vacation, but despite now having been going out for weeks, both Tomoya and Nagisa are still very nervous about it and have not done much to progress their relationship which comes as a shock to their friends. Mei comes back for another visit and after learning of Tomoya's and Nagisa's current stagnant relationship, decides to be their personal cupid of love in order to advance things along. Mei thinks up a whole plan which Nagisa attempts to follow despite it being very embarrassing for her at times. After Tomoya calls Mei out, she runs away, though Nagisa stops Tomoya from chasing after her. With some time left in the day, Tomoya and Nagisa take a walk together.

In an alternative timeline where Tomoya and Tomoyo are dating, Tomoyo becomes student council president, but bad rumors start around the school due to Tomoya's bad reputation. Tomoyo becomes busy during the school festival, and continues to be so while she attempts to save the sakura trees in town. Tomoya realizes that he is holding Tomoyo back from greater things, and despite both sides being reluctant, they break up. Time passes as Tomoyo's reputation builds and Tomoya and Youhei watch on the side through her many accomplishments, one of them being ultimately saving the sakura trees by the winter. At that time, Tomoya and Tomoyo meet and talk for the first time in months and they decide to become a couple again.