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.

When Mei shows up, she cleans her brother's filthy room, but cannot stay at her Youhei's all-boy dorm, so Nagisa offers to have her stay at her home while she is in town. Tomoya and Youhei easily get Kyou to help with the basketball game, and she gets pumped up after a comment about pairing up with such loser guys. For half the game, Tomoya and the others play against first-year rookies, and manage to lead by eleven points, but then the basketball team switches with their starters and the score evens out. In the very last seconds of the game, Tomoya manages to make the last shot and win the game. Afterwards, Mei goes back to her hometown.

After hearing Nagisa talk about the story for the play she wants to perform, Tomoya tries asking Nagisa's parents about it, but they do not know any story like that. After Akio catches Tomoya and Nagisa in the shed, he tells them to leave, and later brings Tomoya aside to tell him about what happened in the past. Ten years prior, Nagisa was running a high fever one snowy day, and in the midst of this, her parents had to work, so they left her alone for a couple of hours. When Akio returned, he found Nagisa collapsed outside as she had been waiting for them to return. Due to Nagisa nearly dying, both of her parents abandoned their jobs and their dreams in order to protect Nagisa. Akio tells Tomoya not to tell either Sanae or Nagisa about the story since he does not want it coming up again. Tomoya goes on a picnic with Nagisa's family, and during a baseball game with some local young boys, Nagisa accidentally confesses her love to Tomoya indirectly.

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 Nagisa visit Youhei, and spend some time talking with Misae and Tomoyo who comes over after them. Later, when Tomoya and Nagisa are talking with Misae privately, Tomoya starts falling asleep. It is shown how when Misae was a first-year in high school, she met a strange boy named Katsuki Shima who says he can grant her one wish in return for her cheering him up years before when he was in the hospital. Misae has a boy she likes named Igarashi, but who unknown to her already has a girlfriend. Igarashi asks Katsuki to tell her this, but he cannot tell her directly and starts crying. Misae sees Igarashi with his girlfriend, and realizes the truth; she runs away, leaving Katsuki behind.

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.

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.

Tomoya and Ushio get back from their trip together. After spending a night with Nagisa's parents, they leave to Tomoya's apartment, where they will both be living from now on. Some time later, Tomoya takes a day off from work and the two meet up with Kouko, whose sister Fuko has been released from the hospital. Afterward, Tomoya and Ushio visit Tomoya's father. Tomoya manages to convince his father into moving back to the countryside with his mother. While Tomoya and Ushio say goodbye to Tomoya's father, a light appears and gets absorbed by Tomoya, while only being noticed by Ushio.

In an alternate timeline, Ryou confesses her love to Tomoya and they both begin dating. However, Tomoya soon notices that Kyou has been acting strange, and confronts her. Kyou admits that she is also in love with him, but never confessed because she was too scared to risk being rejected or hurting Ryou's feelings. This creates an uneasy love triangle among Tomoya, Kyou, and Ryou, leading Tomoya to finally admit that he loves Kyou. Ryou, already knowing that Tomoya loves Kyou more, encourages Kyou to work up the courage to confess. Ryou breaks up with Tomoya with no hard feelings, wanting to cherish both the good and painful memories they had together. Tomoya and Kyou then officially become a couple.