Mei has become worried about her older brother Youhei 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 Kotomi, Tomoyo, Ryou Fujibayashi, and Yukine Miyazawa, but no one can help him. Sanae Furukawa 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 the older sister, instead of the mother, of Nagisa. When Mei meets her brother's so-called girlfriend, Sanae is posing as a student from Tomoya's high school.

Youhei and Sanae go out on a date, accompanied by Tomoya, Nagisa, and Mei. However, Mei still feels that her brother is hopeless even with a dependable girlfriend, and thus still worries about him. Mei remembers that her brother used to be much nicer and worried about her in the past when Mei would get picked on. In an attempt to provoke a brotherly response out of Youhei, Mei lies about coming to the city to meet a guy she likes, and Tomoya later pretends in front of Youhei that he is that person. Despite being shocked in both instances, Youhei does not say anything to Mei. Since she cannot leave while things are the way they are, Mei continues to stay for the time being.

Youhei has not been coming to class lately, causing worry among his friends as well as his sister. Visiting Yukine in the library, Tomoya tells how Youhei quit soccer because of older teammates' bullying. Tomoya, Nagisa, and Mei visit the soccer club, and they try to convince them to let Youhei rejoin. After a grueling task of fetching soccer balls, the club still will not let Youhei back on the team. While the leader of the soccer team makes Mei cry and picks on her, Youhei storms in and starts beating up the entire soccer club with the help of Tomoya. After the soccer club members leave, Tomoya and Youhei have another fight about the protection of Mei. Youhei finally admits he was worried about Mei, and the fight is resolved after Nagisa and Mei interject. The next day; after Mei returns home, Tomoya and Youhei laugh together on the way to school, and Youhei finds out Sanae is Nagisa's mother. Tomoya later recounts to himself how he and Youhei first met.

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 about the autumn festival, Tomoya starts falling asleep. It is shown how Misae was a third-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 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.

After getting over Igarashi, Misae starts hanging out with Katsuki more and starts falling in love with him. Katsuki sneaks into the school to see how Misae doing with her duties as student council president. One day, Katsuki realizes after going to his house with two of Misae's friends, Saki and Yuki, that he is in fact not Katsuki Shima, but a cat who was sent by the dying Katsuki Shima to grant Misae's wish. At the autumn festival, Misae confesses she has come to love Katsuki, but that night he disappears shortly after Misae made her wish for him to always be with her. After Tomoya wakes up, he realizes the cat showed him all this. Later, everyone goes to the autumn festival. Tomoya takes Nagisa there as their date when the cat and Misae show up. Tomoya then tells Misae some things Katsuki did not get a chance to tell her. An orb of light, much like the one Katsuki claimed to possess that supposedly grants a single wish, appears in the night sky.

Tomoya, Nagisa, and Youhei discover 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 Kazuto Miyazawa is the leader of one of the gangs, and a young boy named Yū comes to her to find his older sister who apparently is dating a guy in Kazuto's gang. Youhei pretends to Yū that he is Yukine's brother for the time being, but the truth is later revealed after Yukine takes Yū, along with Tomoya, Nagisa, and Youhei, to a bar where her brother's gang hangs out. Kazuto has been in the hospital since he got into a car accident when he saved a friend. While heading home, three members of the rival gang mistaken Youhei for Kazuto and try to fight him and Tomoya, but Tomoyo intervenes, stopping them single-handedly.

Tomoyo speaks to Yukine and the others about hearing the police will start to get involved in the fight between the two gangs gets any worse. Trying to stave off a major brawl due to a misunderstanding, Yukine goes with Tomoya to try to talk the other gang out of a fight, and the leader settles on a fight between him and Yukine's brother Kazuto. Youhei reluctantly goes to stand in for Kazuto but is incapacitated along with everyone else after eating Sanae's bread. So Tomoya, who did not eat the bread, fights the leader of the opposing gang. Yukine impersonates Kazuto to end the fighting and finally reveals to everyone that did not already know Kazuto has been dead for some time, and his wish was to end the fighting in the town. At the cemetery, Yukine pays respect to her dead brother and the rival gang joins in. With the rivalry resolved and peace restored, Tomoya witnesses an orb of light rising into the sky. Later, Yukine then tells Tomoya, Nagisa, and Youhei about the city's legend of the orbs of light.

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, and she will have to repeat her last year of high school again, unfortunately. Tomoya brought a stuffed dango for Nagisa on her birthday while their friends come over for Christmas Eve. On the day of graduation, as Toshio Koumura decided to retire, 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 re-establish the drama club ends in failure. Tomoya eventually moves out of Nagisa's home to a small apartment of his own; thanks to Ryou, while taking up a job as an electrician with Yusuke. After his first day of work, Tomoya returns to his new home completely exhausted, barely able to stay awake during his dinner with Nagisa.

Working has its ups and downs for Tomoya. He does not want his boss to find out that he has an injured shoulder, in fear that he will lose his new job. Yusuke keeps Tomoya's physical disability a secret. Tomoya promises Nagisa that he will join her at the Founder's Festival, yet work gets busy and while his fellow co-workers would have covered for him, he wanted to prove his worth. He is late for his date and is starting to become too busy to sustain a healthy relationship with Nagisa; although she understands him. Resolving his responsibility, Tomoya gains respect with his co-workers and settles into his job.

Yusuke tells Tomoya a little about his past and how he met Kouko Ibuki in high school. After graduating, Yusuke went on to become a successful singer-songwriter, but ultimately it all came crashing down and he started taking drugs. When he came back to the city and saw Kouko again for the first time in years, he regretted not continuing to sing for her sake. The exciting news is, Tomoya was offered a new position as a manager in a big company, but the deal falls through when his father Naoyuki Okazaki is arrested at bad timing. Tomoya is enraged that his father is still messing up his life. Nagisa manages to calm him down from hurting himself. Tomoya finally proposes to Nagisa, and she accepts.

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, even during the heavy downpour, 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, to which Akio agrees. Months later, Christmas time arrives, and as Nagisa turns 20, 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, including Koumura, to gather at the school and celebrate Nagisa's graduation. Nagisa receives her diploma and finally graduates. Later, they notify Naoyuki and he congratulates them. Tomoya and Nagisa get married afterward while taking a walk on the hill of cherry blossoms.

Tomoya and Nagisa Okazaki are now a married couple living together. Nagisa tries to find work and starts as a waitress at a newly opened family restaurant with Rie Nishina and Sugisaka near the school hill. Tomoya and Akio visit Nagisa at work and scare out a couple of customers who were hitting on Nagisa. Back at home, Nagisa tells Tomoya that the old building of the school they went to is going to be torn down. Knowing that the drama club was in the old building, Tomoya freaks out and admits that he is uncomfortable with all the changes happening in their town. Tomoya and Nagisa visit her parents then Sanae tells them Nagisa is most likely pregnant! Akio gets mad at Tomoya at first, but he congratulates him afterward.

Everyone congratulates Tomoya on becoming a father soon. Nagisa becomes increasingly bedridden due to morning sickness. Nagisa wants to give birth at home, so Sanae introduces Yagi, a midwife who is to assist in the delivery. Sanae later tells Tomoya that giving birth will be difficult because of Nagisa's weak physique and may even put Nagisa's life at risk, so they might have to choose abortion. However, Sanae leaves the choice up to Tomoya and Nagisa. Nagisa learns of her mother's worries, but she decides to go through with the birth. Akio takes Tomoya to a meadow and tells him more about the day when Nagisa nearly died. Akio carried Nagisa to the meadow and prayed for her life, and Nagisa miraculously regained consciousness. Akio tells Tomoya that while many painful and difficult things will happen, he and Sanae will always be there for Tomoya and Nagisa since they are family. Tomoya and Nagisa take a walk by the river and decide on the name Ushio for their child.

Winter comes as Nagisa enters the final months of her pregnancy and some friends come over for New Year's Day. When Kotomi tells her research about 'Another World', Tomoya spontaneously remembers Nagisa's play. On a heavy snow day, Nagisa becomes sick again and goes into labor two weeks early. Tomoya 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 their 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 the entire time, is devastated by this cruel twist of fate. His dream of raising their daughter together as a family is shattered.

Five years later, after leaving Ushio in the care of Akio and Sanae, Tomoya spends his days working long hours, smoking, and drinking. One day, Tomoya and Sanae go out together into town, and she asks him to go with them on a family trip; after Sanae continues to ask him, he accepts. On the day of the trip, he discovers that both Akio and Sanae have left him alone with Ushio. The two spend the next day and night together, but Tomoya finds it difficult to connect with the small child. After Akio and Sanae 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.

While on the trip, Tomoya buys a toy robot he picks out for Ushio to play with after they arrive in the countryside. The next day, after staying at an inn the previous night, Tomoya and Ushio take a walk through the area and come across a field of rape blossom. Ushio plays in the field as Tomoya watches, but Ushio soon loses the robot in the field; they try to look for it but to no avail. Remembering something from his past, Tomoya goes off to another area and meets his grandmother Shino Okazaki, his father's mother. She tells Tomoya how he came here with his father shortly after his mother Atsuko Okazaki died, and also how his father worked very hard to support him over the years. Tomoya finally comes to terms with Naoyuki that he is not a bad father. When they go back to the field where Ushio is, she still cannot find the robot and does not want to stop looking because it was the first thing her father ever gave her. Tomoya realizes his previous mistakes and vows to try his best for Ushio from now on, who is very happy at the prospect of being with her father. On the way home, Tomoya starts telling Ushio about Nagisa for the first time, but memories of Nagisa cause him to break down. After being comforted by Ushio, Tomoya realizes how important the two are for each other, and finally embraces his role as Ushio's father.

Tomoya and Ushio came back from their trip together. After spending a night with Nagisa's parents, they leave for Tomoya's apartment, where they will both be living from now on. Sometime later, Tomoya takes a day off from work and the two meet up with Kouko Yoshino, whose sister Fuko Ibuki has finally been released from the hospital. Afterward, Tomoya and Ushio visit Naoyuki. Tomoya manages to convince his father into moving back to the countryside with his mother Shino. While Tomoya and Ushio happily say goodbye to Naoyuki now that his role as a father has come to an end, an orb of light appears and gets absorbed by Tomoya, while only being noticed by Ushio.

When Tomoya brings Ushio to school he meets her teacher, who is none other than Kyou after seeing Botan her pet boar, and the two soon reacquaint themselves. After that, Tomoya goes to work and Yusuke asks him for Fuko to play with Ushio, since they have become friends after all, and Tomoya agrees. When it is time to sleep, Tomoya uses the "Dango Daikazoku" song to lull Ushio to sleep. Fuko arrives at Tomoya's house to play until the evening when she goes back home as she reminds him about Nagisa. The next day, Kyou tells Tomoya about the annual sports day at school where the parents are to participate as well. He is reluctant about it, but Ushio encourages him, which makes him change his mind. One evening, Ushio is taking a stroll to the new hospital by herself and encounters Fuko on her way. When the latter asks why she does this, Ushio says it is for no real reason. The next day, Tomoya is preparing for the meet at the Furukawa bakery, when Ushio is suddenly struck with a fever, much to the others' shock.

Ushio has the same illness as Nagisa's and Tomoya decides to stay home to take care of her. In case he has to leave home, he arranges for both Akio and Sanae to be able to take his place. Ushio asks Tomoya that she wants to go on a trip like last time, but he tells her that it will happen once she gets better. After Tomoya resigns from his job, Yusuke wishes him the best of luck. Akio offers Tomoya some money, but he declines his kindness and Akio states that every man has something to protect. Tomoya believes that Nagisa's and Ushio's lives are somehow linked to the "changing" in the city. After several months, winter arrives and then Christmas. Ushio's fever has still not broken, and Tomoya seems to be getting sick as well. He begins to hallucinate and sees an illusionary world. Ushio once again asks 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 and it starts snowing, Ushio's fever worsens. Calmly and serenely, she tells Tomoya that she loves him and dies in his arms. Soon after, Tomoya collapses in grief and supposedly dies of shock, and something strange begins to happen.

After failing to create a flying machine to travel to an alternate world, the Girl in the Illusionary World is dying in the snow, and the Junk Robot, created by the girl, regrets having her take the journey. The girl can finally hear the robot and tells it that they once existed in another world. As she hums the tune of "Dango Daikazoku", the illusionary world starts to disappear. As the robot is swept away, the girl calls him "Daddy" and disappears with the world. On the school hill the day Tomoya first met Nagisa, he and the robot become one, he calls after Nagisa, hugs her, and she is glad that he did so. Nagisa brings Tomoya through time, events before Ushio's birth remain the same, and together the voices of Tomoya and the robot 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 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 as a family, finally free of their cursed fate. After five years, Fuko and Kouko are walking to the new hospital to get a checkup. Fuko goes into the woods and spots the girl from the Illusionary World sleeping under a tree. When she approaches, it turns out to be Ushio; Fuko says that she would like to be friends and that the fun is just getting started.

One year before the events of the beginning of the story, Tomoya is beginning his second year in high school, while Nagisa is starting her third year. Nagisa is having trouble making friends as usual, while Tomoya and Youhei are busy being delinquents and carrying out pranks on Kyou, and inadvertently Nagisa's, expense. After Nagisa is knocked out by a falling metal pan that Tomoya and Youhei had set up as a prank for freshmen, a classmate of Nagisa's finally finds the chance to talk with her and they become friends. Nagisa keeps the banner from the prank, one with the message to instill confidence written by Tomoya because she feels it attributed her to make a new friend.

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, Tomoya begins to quite clearly recall a more tragic set of circumstances, a reality which didn't happen due to efforts of the girl in the illusionary world but of which he has a clear memory of. 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.

In an alternate timeline, Ryou confesses her love to Tomoya and they both begin dating. However, Tomoya soon notices that Kyou has been acting strange, and confronts her. Kyou admits that she is also in love with him, but never confessed because she was too scared to risk being rejected or hurting Ryou's feelings. This creates an uneasy love triangle among Tomoya, Kyou, and Ryou, leading Tomoya to finally admit that he loves Kyou. Ryou, already knowing that Tomoya loves Kyou more, encourages Kyou to work up the courage to confess. Ryou breaks up with Tomoya with no hard feelings, wanting to cherish both the good and painful memories they had together. Tomoya and Kyou then officially become a couple.