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.

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. Tomoya and Nagisa later go see Fuko about the club, and he discovers from Nagisa that Fuko is supposedly unconscious in a hospital.

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.

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 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. 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.

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.

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. Kyou initially passes on the chance, but ends up giving in after her sister says she wants to join, and Kotomi joins as well. During the meeting, Kotomi leaves when she hears someone playing the violin, though when she is given the chance to play it, she is painfully horrible.

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

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. While out, Fuko makes an appearance in, but no one remembers her. The next day, Nagisa runs up to Kyou thinking Ryou got in a bus accident, though when they rush to the scene, they find no one was hurt; however, Kotomi has an emotional episode and collapses while screaming out. Kotomi leaves early that day, but when Tomoya, Nagisa and the Fujibayashi twins go to see her later, there is no answer at her house. After they leave, Tomoya goes back and runs into the strange man from earlier; he finds out the man is an acquaintance of Kotomi's parents.

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 ultimately ended up burning her father's important work before anyone could see it. While Kotomi shuts herself in her house, Tomoya comes over and starts cleaning up the garden which is overgrown with grass and weeds. Nagisa, Kyou and Ryou eventually help out too.

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. Kotomi and her friends find out that he is her legal guardian, and that there never were any written notes for the thesis after all. The envelope Kotomi set fire to, and felt so guilty about, was nothing important. The stranger also has a birthday gift for her: her parents' suitcase, which survived the plane crash and was passed from hand to hand for years until he found it. Inside is a teddy bear, Kotomi's gift request to them before they left, and an affectionate letter. Kotomi, holding the bear, is so happy that sparkles literally fill the room, and makes peace with her parents' deaths at last.

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.

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. Kyou continues to set up situations where Tomoya and Ryou are together, such as eating lunch together. Yukine tries to help Tomoya with a charm book, and he performs a charm to get locked in the gym equipment room with Kyou, which ends up happening. Kyou does not act like her usual self while in the room, and thinks that Tomoya may end up trying to have sex with her. Tomoya undoes the charm and the door is opened by one of Kyou's classmates. Tomoya and Tomoyo start to walk home after school, but a a bunch of gang members are at the school's entrance looking to fight Tomoyo.

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 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. When Akio returned, he found Nagisa collapsed outside as she had been waiting for them to return. Due to Nagisa nearly dying, both of her parents abandoned their jobs and their dreams in order to protect Nagisa. Akio tells Tomoya not to tell either Sanae or Nagisa about the story since he does not want it coming up again. Tomoya goes on a picnic with Nagisa's family, and during a baseball game with some local young boys, Nagisa accidentally confesses her love to Tomoya indirectly.

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.

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.