After the previous night's events, Tomoya goes to see if Nagisa is okay, and finds out that she has been physically weak all her life. While walking back from the bakery, Tomoya helps get a strange electrician out of a jam and he gives Tomoya his card, finding his name to be Yusuke Yoshino; Youhei later reveals that Yusuke is a retired professional musician. After school the next day, Tomoya helps Nagisa get more self-confidence for the drama club by acting as a new member of the club asking questions.

In order to help Fuko out, Tomoya and Nagisa take her to stay at Nagisa's house for the time being. Nagisa's family helps with carving more starfish out of wood, and at school Tomoya and Nagisa help with passing them out to students. Later, Fuko talks about how she has wanted to attend classes, but has never been able to. Tomoya makes arrangements with Youhei, Kyou, and Ryou to act as classmates in Fuko's very first high school class, and even Sanae comes to act as the teacher.

Kotomi is still trying to play the violin, but has not improved at all; in short, her playing is painful to anyone listening. Kyou gets the idea to have Kotomi play at her first violin recital after school the day after tomorrow, and in the mean time Kotomi can practice. The day before the recital, Tomoya visits Kotomi at the school's library and eats her delicious homemade apple pie. Shortly after, Tomoya falls asleep and has a very strange dream. At the recital, Kyou blackmails several students into coming with her position as a class representative. In the end, Kotomi did not improve at all, and the recital was still very painful to listen to. When Kotomi and her friends are going home, a strange man approaches Kotomi, though leaves shortly after; Kotomi was terrified of him

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.

After Nagisa finds out about her parents' secret past, she cannot take her mind off how she ruined their dreams, and becomes emotional and depressed. On the day of the school festival, the whole theater club realizes that Nagisa is not herself, and try to cheer her up, but to no success. As the performance starts, Nagisa breaks down, but with encouragement from Akio, who said that Sanae's and his dream was for Nagisa to make her dream come true, the play was a huge success. The next day as the sun is setting, Tomoya finally confesses his love to Nagisa in the club room. This comes as a shock for Nagisa, causing her to cry tears of joy.

Mei has become worried about her older brother since he still does not have a plan after high school, and comes to stay at Nagisa's for the time being. Based on a fleeting comment by Youhei, Tomoya gets the idea to ask a girl to pose as his girlfriend so Mei will stop worrying about him. Youhei goes around with Tomoya and Nagisa asking Ryou, Tomoyo, Kotomi, and Yukine, but no one can help him. Sanae overhears Youhei's trouble and decides to be his fake girlfriend if it will help push him in the right direction in life. Youhei, however, still believes her to be Nagisa's older sister. When Mei meets her brother's "girlfriend", Sanae is posing as a student from Tomoya's high school.

Youhei has not been coming to class lately, and his friends and Mei are worrying about his situation. Mei, Tomoya, and Nagisa visit the soccer club, and try to convince them to let Youhei rejoin. After a grueling task of fetching soccer balls, the club still will not let Youhei back on the team. While the leader of the soccer team makes Mei cry and picks on her, Youhei storms in and starts beating up the entire soccer club with the help of Tomoya. After the soccer team members leave, Tomoya and Youhei have another fight about the protection of Mei. Youhei finally admits he was worried about Mei, and the fight is resolved after Mei and Nagisa interject. Tomoya later recounts to himself how he and Youhei first met.

Tomoya, Nagisa, and Youhei finally find out that Yukine is respected by the two rival gangs in the city since she helps both sides' members after they get hurt. Her older brother is the leader of one of the gangs, and a young boy named Yu comes to her to find his older sister who apparently is dating a guy in Yukine's brother's gang. Youhei tells Yu that he is Yukine's brother for a time, but the truth is later revealed after Yukine takes Yu, along with Tomoya, Nagisa, and Youhei, to a bar where her brother's gang hangs out. Yukine's brother has been in the hospital since he saved a friend and got in a car accident. While heading home, three members of the rival gang think Youhei is Yukine's brother and try to fight him and Tomoya, but Tomoyo intervenes, stopping them single-handedly.

Tomoyo speaks to Yukine and the others about hearing that the police will start to get involved in the fight between the two gangs if it gets any worse. Trying to stave off a major brawl, Yukine goes with Tomoya to try to talk the other gang out of a fight, and the leader settles on a fight between him and Yukine's brother Kazuto. Youhei reluctantly goes to stand in for Kazuto, but is incapacitated along with everyone else but Tomoya after eating Sanae's bread, so Tomoya fights the leader of the opposing gang. Yukine impersonates Kazuto to end the fighting, and finally reveals to everyone that did not already know that Kazuto has been dead for some time, and his wish was to end the fighting in the town. At the cemetery, Yukine pays respect to her dead brother and the rival gang joins in. With the rivalry resolved and peace restored, Tomoya witnesses a glow rising into the sky.

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.