Tomoya and Nagisa convince Kouko that Fuko would wish for her to get married despite Fuko's condition. They talk to the school's administration after finding out Kouko would like to get married on the school grounds. Kouko informs them that Fuko's condition has gotten worse, and she may not awaken from her coma, while Youhei shares his observation that some students cannot see Fuko and others are beginning to forget her and the presents she gave them.

Tomoya, Nagisa, and Fuko spend the night at school having a pre-celebration for Youko's wedding. In the morning, Tomoya and Nagisa have forgotten about Fuko and cannot see her. Both Tomoya and Nagisa later feel that there is something important that they are forgetting, and finally remember about Youko's wedding, which is also when they are able to see Fuko again. On the wedding day, initially the only students to arrive were Tomoya, Nagisa, and Fuko, but after the ceremony it is shown that everyone who had received a starfish came to the wedding. Fuko ultimately disappears after thanking Tomoya and Nagisa for what they have done, and congratulating her older sister. A rumor still persists at Tomoya's school of Fuko as a cute girl who is constantly running through the school.

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.

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.

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 and his friends are nearing graduation, and are discussing what they will be doing after they graduate. Kyou wishes to be a kindergarten teacher, Ryou hopes to go to a nursing school, Kotomi wants to study in America, and Youhei aspires to be a model. Tomoya still has not decided on what to do yet. Nagisa's sickness returns, making her unable to go to school and take exams. On the day of graduation, Tomoya returns home to Nagisa who wishes to take a walk with him, while holding hands.

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.