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 forgets 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 Kouko's wedding, as the two and Fuko become closer. The next 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 Kouko'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. Kouko and Yusuke walk down the campus as everyone applauds them. Fuko ultimately disappears afterwards, thanking Tomoya and Nagisa and congratulating her older sister. A rumor still persists at the school of Fuko as a cute girl who is constantly running through the school. Tomoya believes Fuko will awaken someday.

Since no new members have joined the drama club, Tomoya goes to talk with Kotomi once again about joining. Tomoya takes her around the 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, he 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 suddenly leaves when she hears someone playing the violin in a nearby club room. Yet when she is offered a 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 in two days, obliging Kotomi to practice in the meantime. 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, the school; including Akio, Sanae, and Misae Sagara; the landlady of Youhei's dorm came to listen. 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, stating that he is a "bad man".

Kotomi returns the violin to Rie Nishina and becomes friends with her. Kotomi changes her usual routine and starts attending her classes. Kyou invites Tomoya, Nagisa, Kotomi, and Ryou to go out together as a group and have fun at a local carnival. While they are at a claw crane, Fuko makes an appearance, but no one seems to remember 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 when Kotomi sees the accident, she has an emotional episode and collapses while screaming out. Kotomi leaves early that day, but when Tomoya, Nagisa, Kyou, and Ryou 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 gentleman is an acquaintance of Kotomi's parents. Tomoya ends up going into Kotomi's house and finds her in a room with newspaper clippings on the wall reporting on the death of Kotomi's parents. Tomoya then finally remembers that he met Kotomi years ago when he was a child.

Tomoya realizes that he met Kotomi as a child, though until now 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 suddenly must leave for a business trip. Later that day, Kotomi is visited by an acquaintance of her parents (the gentleman) who tells her that they were killed in a plane crash. Kotomi ultimately ends up burning her father's important thesis about discovering 'Another World' before anyone could see it. From then on, Tomoya stops coming to her house, as Kotomi dedicates herself to follow her parents' footsteps. While Kotomi shuts herself in her house, Tomoya comes over and starts cleaning up the overgrown garden before her birthday. Nagisa, Kyou, and Ryou eventually help out as well. In the end, Kotomi is happy with everyone's generosity.

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, Nagisa, Kyou, and Ryou are all waiting for her. The mysterious gentleman whom she was so frightened of, believing he wanted to take 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 other copy notes for the thesis after all. The envelope Kotomi burned and felt so guilty about was actually a teddy bear catalog. The gentleman also has a birthday gift for her, which is her parents' suitcase, that survived the plane crash and was passed from hand to hand around the world for years until he found it. Inside is a teddy bear, Kotomi's gift request to her parents before they left, and an affectionate letter. While Kotomi is holding the teddy bear, the room fills with orbs of light, and she, at last, makes peace with her parents' deaths.

To help Nagisa reform the drama club, her friends offer their names to get enough members to qualify, but they still need an advisor with them for the club, which leads them to ask Toshio Koumura. However, he is already meant to be the advisor for the choir club, so Nagisa goes to talk with Rie about which club Koumura should advise. The next day, Nagisa finds a threatening letter on 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 and Kyou. Tomoya and Youhei go to Yukine to kill time during school, and Yukine gives Youhei an idea related to basketball. Later on, two captains of the judo club are pestering Tomoyo to join. Fuko appears but not too much help, yet Tomoya manages to take Tomoyo with him to get away from the captains. The next day, Youhei approaches Tomoya and Nagisa about playing in a basketball match to get the choir club to back down, but Tomoya continuously refuses his offer. After school, Tomoya and Nagisa meet Youhei's younger sister Mei Sunohara.

When Mei shows up, she cleans her brother's filthy room, but Misae said she cannot stay at Youhei's all-boys 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. They bring the choir club over to watch the game. 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 scores even out. In the very last seconds of the game, Tomoya manages to make the last shot thanks to Nagisa's voice, and wins the game. Afterward, Mei goes back to her hometown.

After watching the basketball game, the choir club decide to share Koumura with the drama club, but the student council will not allow it. Nagisa collapses at school and is absent for a few days following. Then, Tomoya believes if Tomoyo becomes student council president she can make arrangements and revive the drama club. 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 grimoire, and he casts a spell 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 wrongly concludes that Tomoya may try to have sex with her. Tomoya undoes the spell and the door is opened by one of Kyou's classmates. Tomoya and Tomoyo start to walk home after school, but a bunch of gang members is at the school's entrance looking to fight Tomoyo. Fuko temporarily interrupts the fight. After the fight starts, teachers from the school arrive and break it up; Tomoya takes the blame for it to protect Tomoyo, and is sentenced to suspension as a consequence.

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 Naoyuki, he does not answer her. On Sunday, when Tomoyo is making him lunch, Kotomi, Kyou, and Ryou 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, and desire to protect the cherry blossom trees. 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. Tomoyo realizes that Tomoya is in love with Nagisa, and both Kyou and Ryou break into tears. Ultimately, Tomoyo becomes the student council president.

The drama club is finally revived and Koumura is shared with the choir club, thanks to Tomoyo. Tomoya's homeroom teacher goes to Tomoya's house to ask Naoyuki about his son's future, but Naoyuki says that it is something Tomoya has to decide for himself. Seeing the way Tomoya and Naoyuki are, 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 of the "Girl in the Illusionary World" for the play she wants to perform, Tomoya tries asking Nagisa's parents and Yukine about it (which seems familiar to him), but they do not know any story like that; Fuko appears unexpectedly. 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 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.

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 drama club realizes that Nagisa is not herself, and tries to cheer her up, but to no success. As the performance starts, Nagisa breaks down, but with encouragement from Akio, who said that his dream, as well as that of Sanae, was for Nagisa to make her dream come true, Tomoya also assures Nagisa, and the play about the Girl in the Illusionary World was a huge success! Naoyuki came to see them play too. 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.

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 helps out with the bakery. After learning of Tomoya and Nagisa's current stagnant relationship, Mei decides to be their personal cupid of love 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 while finally holding hands.

In an alternative timeline where Tomoya and Tomoyo are dating, Tomoyo becomes student council president, but bad rumors start around the school due to Tomoya's bad reputation. Tomoyo becomes busy during the school festival and continues to be so while she attempts to save the cherry blossom trees in town. A male student (Yuji Suehara) makes Tomoya realize that he is holding Tomoyo back from greater things, and despite both sides being reluctant, they break up. Time passes as Tomoyo's reputation builds and Tomoya and Youhei watch on the side through her many accomplishments, one of them being ultimately saving the cherry blossom trees by the winter. While on the way home after attending his high school graduation ceremony, Tomoya sees Tomoyo waiting for him along the snowy road lined by the cherry trees. They talk for the first time in months. From Tomoya's view, his expectation is that their lives have diverged, never to come together again, but he is surprised when Tomoyo expresses her desire to be with him again. Tomoya tries to dissuade her from making that choice, but her mind is made up; she would rather be with him. Tomoya and Tomoyo become a couple again.