Since no new members have joined the drama club, Tomoya goes to talk with Kotomi once again about joining. Tomoya takes her around school and helps her introduce herself to people to make more friends. Tomoya takes Kyou, Ryou, and Kotomi to the drama room after school, and after a round of introductions, Tomoya asks them to join the club. Kyou initially passes on the chance, but ends up giving in after her sister says she wants to join, and Kotomi joins as well. During the meeting, Kotomi leaves when she hears someone playing the violin, though when she is given the chance to play it, she is painfully horrible.

Kotomi returns the violin to Rie Nishina and becomes friends with her. Kotomi changes her usual routine and starts attending her classes. Due to Kyou's idea, she, Ryou, Kotomi, Nagisa, and Tomoya go out together as a group and have fun in town. While out, Fuko makes an appearance in, but no one remembers her. The next day, Nagisa runs up to Kyou thinking Ryou got in a bus accident, though when they rush to the scene, they find no one was hurt; however, Kotomi has an emotional episode and collapses while screaming out. Kotomi leaves early that day, but when Tomoya, Nagisa and the Fujibayashi twins go to see her later, there is no answer at her house. After they leave, Tomoya goes back and runs into the strange man from earlier; he finds out the man is an acquaintance of Kotomi's parents.

In order to help Nagisa reform the drama club, her friends offer their names in order to get enough members to qualify, but they still need a teacher to advice them with the club, which leads them to ask Toshio Koumura. However, he is already meant to be the adviser for the choir club, so Nagisa goes to talk with Rie Nishina about which club Koumura should advise. The next day, Nagisa finds a threatening letter in her desk, and Youhei finds out that it was Rie's friend Sugisaka who is behind it. After talking with Nagisa about Rie's past, Nagisa chooses to give up on reforming the drama club, though this does not sit well with Youhei. Tomoya and Youhei go to Yukine Miyazawa to kill time during school, and Yukine gives Youhei an idea related to basketball. The next day, Youhei approaches Tomoya and Nagisa about playing in a basketball match in order to get the choir club to back down, but Tomoya continuously refuses his offer.

After watching the basketball game, the choir club decides to share Koumura with the drama club, but the student council will not allow it. Nagisa collapses at school and cannot come to school for a few days. During this time, Tomoyo starts waking up Tomoya and Youhei before classes start so they will not be late anymore. Kyou continues to set up situations where Tomoya and Ryou are together, such as eating lunch together. Yukine tries to help Tomoya with a charm book, and he performs a charm to get locked in the gym equipment room with Kyou, which ends up happening. Kyou does not act like her usual self while in the room, and thinks that Tomoya may end up trying to have sex with her. Tomoya undoes the charm and the door is opened by one of Kyou's classmates. Tomoya and Tomoyo start to walk home after school, but a a bunch of gang members are at the school's entrance looking to fight Tomoyo.

Nagisa and her friends continue to practice for the play, such as reciting tounge twisters, choosing which music to use for the play, lighting, and stage direction. Nagisa's father rents a play on video, and Nagisa finds it very touching, plus it was the first play she ever saw. Tomoya and Akio try to find the script of the play that Nagisa is going to perform in the shed, but do not find it. The drama club has a practice the day before the school festival is to begin and it goes well. The night before the school festival, Nagisa looks for a flashlight in the shed, but bumps into some boxes and discovers photographs and diaries of her parent's pasts.

Tomoya tries to convince Akio to talk to him about his decision to marry Nagisa. Akio, however, will only talk to him if he can get a decent hit with a baseball match. Tomoya continues to practice hitting the ball until he gets good enough to face Akio again. He finally hits a home run, and runs over to Akio to beg him to let Nagisa be with him; Akio agrees. Christmas time arrives, and as Nagisa turns twenty, she has her first drink of sake; when she is drunk, she accuses Tomoya of being attracted to Sanae. Nagisa's fever goes up again, causing her to become absent from school, but not enough to repeat another year. Tomoya soon organizes with some of their friends and previous classmates to gather at the school and celebrate Nagisa's graduation. Nagisa receives her diploma and graduates. Tomoya and Nagisa get married soon after.

Nagisa and Tomoya are now a married couple living together. Nagisa tries to find work and starts working in a family restaurant with Nishina. Akio and Tomoya visit Nagisa at work and scare out a couple of customers who were hitting on Nagisa. Nagisa tells Tomoya that the old building of the school they went to is going to be torn down. Knowing that the drama club was in the old building, Tomoya freaks out and admits that he is uncomfortable with all the changes happening in their town. Tomoya and Nagisa visit Akio and Sanae, who tells them Nagisa is most likely pregnant. Akio gets angry at Tomoya at first, but he congratulates him afterwards.