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.

Nagisa admits to wanting to restart the drama club, and Tomoya helps Nagisa to create advertisement posters which they place around school. At school that day, Tomoya meets two other girls: a strange genius named Kotomi Ichinose, and a first-year named Fuko Ibuki. Later that day, Nagisa finds out Tomoya used to play basketball, and invites him to play a game the next day. However, it is later revealed that his father injured Tomoya's arm in a fight; as a result, he is unable to play basketball anymore.

During the time that Tomoya is suspended from school, Tomoyo continues to come to his house, wake him up, and make him breakfast, though when she tries to ask him about his relationship with his father, he does not answer her. On Sunday when Tomoyo is making him lunch, Kyou, Ryou, and Kotomi arrive each bringing a bunch of food, and even Fuko appears with food; Tomoya ends up eating everything. Once back at school, he finds out how Tomoyo's reputation is dropping due to rumors of her as a gang leader, and arranges for Tomoyo to compete against several school sports clubs to boost her reputation. After school, Tomoyo tells Tomoya about her family situation and how her brother risked his life to keep their parents from divorcing. Nagisa finally comes back to school and is welcomed by her friends. During a tennis match between Tomoyo and a male tennis club member, a stray ball hits Nagisa on the leg, and Tomoya overprotects her, showing everyone how devoted he is to her.

The drama club is finally re-established and Koumura is shared with the choir club. Tomoya's home room teacher goes to Tomoya's house to ask his father about his future, but Tomoya's father says that is something that Tomoya has to decide for himself. Seeing the strained relationship between Tomoya and his father, Nagisa offers to have Tomoya stay over at her house for the time being, which he accepts. After coming home from school, Tomoya finds several small kids in Nagisa's house, and finds out Sanae is instructing them in a cram school. Nagisa confides to Tomoya that she feels she did something really bad to her parents in the past, but she cannot remember what it is, and her parents say that she must be imagining it.

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.

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.

Tomoya tells Ushio of the past events that happened from when he first met Nagisa, until after Ushio is born and Nagisa survives. When Ushio falls asleep during the story, he begins to quite clearly recall a more tragic set of circumstances. At the end of this retelling, Tomoya, with Ushio and Fuko who are both asleep, are shown under a tree at the present time having a picnic. Ushio wakes up, just before Nagisa calls the three of them, saying that it is time to head home.