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.

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.

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.

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.

Mei has become worried about her older brother since he still does not have a plan after high school, and comes to stay at Nagisa's for the time being. Based on a fleeting comment by Youhei, Tomoya gets the idea to ask a girl to pose as his girlfriend so Mei will stop worrying about him. Youhei goes around with Tomoya and Nagisa asking Ryou, Tomoyo, Kotomi, and Yukine, but no one can help him. Sanae overhears Youhei's trouble and decides to be his fake girlfriend if it will help push him in the right direction in life. Youhei, however, still believes her to be Nagisa's older sister. When Mei meets her brother's "girlfriend", Sanae is posing as a student from Tomoya's high school.

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.

Tomoya, Nagisa, and Youhei finally find out that Yukine is respected by the two rival gangs in the city since she helps both sides' members after they get hurt. Her older brother is the leader of one of the gangs, and a young boy named Yu comes to her to find his older sister who apparently is dating a guy in Yukine's brother's gang. Youhei tells Yu that he is Yukine's brother for a time, but the truth is later revealed after Yukine takes Yu, along with Tomoya, Nagisa, and Youhei, to a bar where her brother's gang hangs out. Yukine's brother has been in the hospital since he saved a friend and got in a car accident. While heading home, three members of the rival gang think Youhei is Yukine's brother and try to fight him and Tomoya, but Tomoyo intervenes, stopping them single-handedly.

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.

Shortly after his graduation, Tomoya decides to be more independent, and works toward this goal by first taking up a job at the bakery. Meanwhile, Nagisa has begun her new school year, although she makes few friends and her attempt to reestablish the theater club ends in failure. Tomoya eventually moves out of Nagisa's home to a small apartment of his own, while taking up a job as an electrician with Yusuke Yoshino. After his first day of work, Tomoya returns to his home completely exhausted, barely able to stay awake during his dinner with Nagisa.

Winter comes and Nagisa enters the final months of her pregnancy, but she becomes sick again. On a snowy day, Nagisa goes into labor two weeks early and her family, unable to transport her to a hospital in time, is forced to have her give birth at home. After an excruciating process, Nagisa successfully gives birth to her daughter, Ushio, but the delivery and her illness combined take their toll on her and Nagisa dies moments after seeing her newborn baby. Tomoya, who has stayed by her side for the entire time, does not take the sudden turn of events well. His dream of raising their daughter together as a family is shattered.

Five years after Tomoya left Ushio with Sanae and Akio, he spends his days at work and spending money on smoking and drinking. Sanae and Tomoya go out together into town, and she asks him to go with her and Akio on a family trip; after Sanae continues to ask him, he accepts. The day of the trip, he discovers that both Sanae and Akio have left him and Ushio alone together. The two spend the next day and night together, and when Sanae and Akio still do not show up, Tomoya asks Ushio if she would be willing to still go on a trip, even if it was only with a person like him. The two decide to take the trip by themselves and, as they walk, Tomoya wonders where they are headed.

Ushio's fever does not back down and Tomoya decides to stay home to take care of her. In case he had to leave home, he calls for both Akio and Sanae to take his place. Ushio tells Tomoya that she wants to go on a trip again like last time, but he declines and tells her that it will happen once she gets better. After resigning from his work, Akio offers him some money, but Tomoya declines his kindness and Akio states that every man has something to protect. After several months, winter arrives, and Ushio's fever still does not back down, and Tomoya seems to be getting sick too. Ushio once again ask Tomoya to go on a trip, and he ultimately accepts thinking that he might not be able to fulfill another promised wish. After they leave the house, Ushio's fever worsens, and she dies in his arms right after telling her father that she loves him. Soon after, Tomoya collapses as well.

The girl in the Illusionary World is dying in the snow, and the robot regrets having her take the journey. The girl can finally hear the robot, and tells him that they once existed in another world. As she hums the tune of "Dango Daikazoku", the Illusionary World starts to collapse. As the robot is swept away, the girl calls him "Papa" and disappears with the world. Back at the hill, Tomoya calls after Nagisa, and she is glad that he did so. Nagisa brings Tomoya through time, and together the voices of the robot and Tomoya note the end of his long journey. Tomoya awakens to Ushio's birth, but this time, Nagisa miraculously survives. After Nagisa watches Tomoya give Ushio her first bath, she and Tomoya see that countless orbs of light are floating throughout the city outside the window. They both sing to Ushio and from then on, Tomoya and Nagisa experience a happy life raising their daughter together, finally free of their cursed fate.