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

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 runs into Fuko again at school, and she tries to invite him to her older sister's upcoming marriage ceremony, but Tomoya is not interested. Tomoya gets Youhei to help reform the drama club by bribing him with bread from Nagisa's family bakery. Nagisa tries to get the help of Ryou and Kyou in reforming the drama club, and Tomoya even tries to ask Tomoyo and Kotomi if they would like to join; Tomoyo is trying to become student council president, and Kotomi does not give an answer

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 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

Tomoya and Nagisa convince Kouko that Fuko would wish for her to get married despite Fuko's condition. They talk to the school's administration after finding out Kouko would like to get married on the school grounds. Kouko informs them that Fuko's condition has gotten worse, and she may not awaken from her coma, while Youhei shares his observation that some students cannot see Fuko and others are beginning to forget her and the presents she gave them

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

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

Since no new members have joined the drama club, Tomoya goes to talk with Kotomi once again about joining. Tomoya takes her around school and helps her introduce herself to people to make more friends. Tomoya takes Kyou, Ryou, and Kotomi to the drama room after school, and after a round of introductions, Tomoya asks them to join the club

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

Kotomi returns the violin to Rie Nishina and becomes friends with her. Kotomi changes her usual routine and starts attending her classes. Due to Kyou's idea, she, Ryou, Kotomi, Nagisa, and Tomoya go out together as a group and have fun in town

Tomoya realizes that he met Kotomi as a kid, though only she had remembered. Back then, Tomoya had often visited Kotomi, and was her only friend. Around this time on Kotomi's birthday, her parents left for business reasons, and later that day she finds out they were killed in a plane crash

Kotomi finally leaves the house to find that Tomoya worked in the garden all night long and had fallen asleep. When she returns to school, Tomoya, Kyou, Ryou and Nagisa are all waiting for her. The mysterious stranger whom she was so frightened of, believing he wanted to steal her parents' thesis, is there as well

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

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

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

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

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 hearing Nagisa talk about the story for the play she wants to perform, Tomoya tries asking Nagisa's parents about it, but they do not know any story like that. After Akio catches Tomoya and Nagisa in the shed, he tells them to leave, and later brings Tomoya aside to tell him about what happened in the past. Ten years prior, Nagisa was running a high fever one snowy day, and in the midst of this, her parents had to work, so they left her alone for a couple of hours

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

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