After getting over Igarashi, Misae starts hanging out with Katsuki more and starts falling in love with him. One day, Katsuki realizes after going to his house with two of Misae's friends that he is in fact not Katsuki Shima, but a cat who was sent by the dying Katsuki Shima to grant Misae's wish. At the autumn festival, Misae confesses she has come to love Katsuki, but that night he disappears shortly after Misae made her wish for him to always be with her. After Tomoya wakes up, and realizes the cat showed him all this, Tomoya later tells Misae some things Katsuki did not get a chance to tell her.

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.

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.

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.