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.

Tomoya and Nagisa invite Fuko's older sister Kouko to the Founder's Festival. In the meantime, Fuko hands out more carved starfish to students at the festival, and her fan club helps spread the word about Kouko's wedding too. Nagisa and Tomoya meet Tomoyo, who is wearing a bear suit to find people who are causing trouble, and manages to knock Youhei out a window for bothering a girl. When Kouko finally comes, she cannot see or hear her sister.

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.

Summer vacation is now over and the second semester has started at Tomoya's school. Nagisa's father Akio asks Tomoya to form a baseball team for a local game against the neighboring shopping district team. Tomoya is able to recruit Kyou and Kotomi from the drama club, Youhei and his younger sister Mei, Tomoyo, Misae, and Yusuke. Tomoya's team manages to get an early lead, but Akio's leg gets injured by a flying bat, and Nagisa fills in for her father as the pitcher. The other team catches up near the end, and it comes down to the final inning when Tomoya scores an RBI, winning the game.

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.

Shortly after his graduation, Tomoya decides to be more independent, and works toward this goal by first taking up a job at the bakery. Meanwhile, Nagisa has begun her new school year, although she makes few friends and her attempt to reestablish the theater club ends in failure. Tomoya eventually moves out of Nagisa's home to a small apartment of his own, while taking up a job as an electrician with Yusuke Yoshino. After his first day of work, Tomoya returns to his home completely exhausted, barely able to stay awake during his dinner with Nagisa.

Working has its ups and downs for Tomoya. He does not want his boss to find out that he has an injured shoulder, in fear that he will lose his new job. He promises Nagisa that he will join her at the Founder's Festival, yet work gets busy and while his fellow co-workers would have covered for him, he wanted to prove his worth. He is late for his date, and is starting to become too busy to sustain a healthy relationship with Nagisa. He gains respect with his co-workers and settles into his job.

Yusuke tells Tomoya a little about his past and how he met Kouko in high school. After graduating, Yusuke went on to become a successful singer-songwriter, but ultimately it all came crashing down and he started taking drugs. When he came back to the city and saw Kouko again for the first time in years, he regretted not continuing to sing for her sake. Tomoya is offered a new position as a manager in a new electrician firm, but the deal falls through when his father is arrested. Tomoya is enraged that his father is still managing to mess up his life. Tomoya finally proposes to Nagisa, and she accepts.

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 becomes increasingly bedridden due to morning sickness. Nagisa wants to give birth at home, so Sanae introduces Yagi, a midwife who is to assist in the delivery. Sanae later tells Tomoya that giving birth will be difficult because of Nagisa's weak physique and may even put Nagisa's life in danger, so they might have to choose abortion. However, Sanae leaves the choice up to Tomoya and Nagisa. Nagisa learns of her mother's worries, but she decides to go through with the birth. Akio takes Tomoya to a meadow and tells him more about the day when Nagisa nearly died. Akio carried Nagisa to the meadow and prayed for her life, and Nagisa miraculously regained consciousness. Akio tells Tomoya that while many painful and difficult things will happen, he and Sanae will always be there for Tomoya and Nagisa since they are family. Nagisa and Tomoya take a walk by the river and decide on the name Ushio for their child.

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.

When Tomoya brings Ushio to school he meets her teacher, who is none other than Kyou Fujibayashi and they have a conversation. After that, Tomoya goes to work and Yoshino asks him for Fuko to play with Ushio, since she likes her. Tomoya agrees to this and Fuko arrives at his house to play until the evening when she goes back home. When it is time to sleep, Tomoya uses Nagisa's song to lull Ushio to sleep. The next day, Kyou tells Tomoya about sports day at school where the parents are to participate as well. He is reluctant about it, but Ushio encourages him, which makes him change his mind. One evening, Ushio is taking a stroll to the new hospital by herself and encounters Fuko on her way. When the latter asks why she does this, Ushio says it is for no real reason. The next day, Tomoya is preparing for the meet at the Furukawa bakery with Sanae and Akio, when Ushio is suddenly struck with a fever, much to the others' shock.

Ushio's fever does not back down and Tomoya decides to stay home to take care of her. In case he had to leave home, he calls for both Akio and Sanae to take his place. Ushio tells Tomoya that she wants to go on a trip again like last time, but he declines and tells her that it will happen once she gets better. After resigning from his work, Akio offers him some money, but Tomoya declines his kindness and Akio states that every man has something to protect. After several months, winter arrives, and Ushio's fever still does not back down, and Tomoya seems to be getting sick too. Ushio once again ask Tomoya to go on a trip, and he ultimately accepts thinking that he might not be able to fulfill another promised wish. After they leave the house, Ushio's fever worsens, and she dies in his arms right after telling her father that she loves him. Soon after, Tomoya collapses as well.