On the way to school one day, Tomoya Okazaki meets a strange girl talking to herself named Nagisa Furukawa. Later in the day, Tomoya has a conversation with Nagisa during lunch and learns that she is repeating her last year of high school, and wants to join the now-disbanded drama club. After school, Tomoya goes to Nagisa's family bakery and meets her parents; he is invited to have dinner with them.

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.

More people from school are not able to see Fuko anymore and now even those close to Fuko in the past are beginning to forget about her. First Youhei forget after he goes to see her in the hospital, followed by Kyou and Ryou. Tomoyo manages to remember with Tomoya's help however. Later, Youhei manages to remember Fuko for a moment, but is unable to remember any more. Tomoya and Nagisa buy Fuko a birthday party set to cheer her up. When they get back to the bakery, they discover that Nagisa's father has forgotten Fuko, and while Nagisa's mother has not forgotten completely, she cannot see her anymore. Tomoya and Nagisa decide to take Fuko back to school for now.

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.

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.

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.

It is now during summer vacation, but despite now having been going out for weeks, both Tomoya and Nagisa are still very nervous about it and have not done much to progress their relationship which comes as a shock to their friends. Mei comes back for another visit and after learning of Tomoya's and Nagisa's current stagnant relationship, decides to be their personal cupid of love in order to advance things along. Mei thinks up a whole plan which Nagisa attempts to follow despite it being very embarrassing for her at times. After Tomoya calls Mei out, she runs away, though Nagisa stops Tomoya from chasing after her. With some time left in the day, Tomoya and Nagisa take a walk together.

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.

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.

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 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.