Summer vacation is now over and the second semester has started at Tomoya's school. Nagisa's father Akio asks Tomoya to form a baseball team for a local game against the neighboring shopping district team. Tomoya is able to recruit Kyou and Kotomi from the drama club, Youhei and his younger sister Mei, Tomoyo, Misae, and Yusuke. Tomoya's team manages to get an early lead, but Akio's leg gets injured by a flying bat, and Nagisa fills in for her father as the pitcher. The other team catches up near the end, and it comes down to the final inning when Tomoya scores an RBI, winning the game.
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.
Yohei and Sanae go out on a date, accompanied by Mei, Tomoya and Nagisa. During the date the group witnesses a young girl being bullied by some slightly older boys. The scene is resolved by the girls older brother rushing in to help his sister. Mei remembers how Yohei used to be like that, but once he joined the football club he didn't seem to care about her any more. The group then tries to provoke a brotherly response from Yohei, to get him to stand up for his sister; Tomoya pretends to be romantically interested in Mei, but despite being shocked, Yohei doesn't say anything to oppose them. Mei decides to stay a little while longer, as she can't leave things the way that they are.
Youhei has not been coming to class lately, and his friends and Mei are worrying about his situation. Mei, Tomoya, and Nagisa visit the soccer club, and 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 team 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 Mei and Nagisa interject. 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, 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.
After getting over Igarashi, Misae starts hanging out with Katsuki more and starts falling in love with him. One day, Katsuki realizes after going to his house with two of Misae's friends 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, and realizes the cat showed him all this, Tomoya later tells Misae some things Katsuki did not get a chance to tell her.
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.
Tomoyo speaks to Yukine and the others about hearing that the police will start to get involved in the fight between the two gangs if it gets any worse. Trying to stave off a major brawl, 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 but Tomoya after eating Sanae's bread, so Tomoya fights the leader of the opposing gang. Yukine impersonates Kazuto to end the fighting, and finally reveals to everyone that did not already know that 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 a glow rising into the sky.
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.
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. He 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. He gains respect with his co-workers and settles into his job.
Yusuke tells Tomoya a little about his past and how he met Kouko 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. Tomoya is offered a new position as a manager in a new electrician firm, but the deal falls through when his father is arrested. Tomoya is enraged that his father is still managing to mess up his life. 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 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; Akio agrees. Christmas time arrives, and as Nagisa turns twenty, 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 to gather at the school and celebrate Nagisa's graduation. Nagisa receives her diploma and graduates. Tomoya and Nagisa get married soon after.
Nagisa and Tomoya are now a married couple living together. Nagisa tries to find work and starts working in a family restaurant with Nishina. Akio and Tomoya visit Nagisa at work and scare out a couple of customers who were hitting on Nagisa. 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 Akio and Sanae, who tells them Nagisa is most likely pregnant. Akio gets angry at Tomoya at first, but he congratulates him afterwards.
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 in danger, 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. Nagisa and Tomoya take a walk by the river and decide on the name Ushio for their child.
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.
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 flowers. 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 died, and Shino tells Tomoya how his father worked very hard to support him over the years. Tomoya finally comes to terms with his father, and realizes 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.
Tomoya and Ushio get back from their trip together. After spending a night with Nagisa's parents, they leave to Tomoya's apartment, where they will both be living from now on. Some time later, Tomoya takes a day off from work and the two meet up with Kouko, whose sister Fuko has been released from the hospital. Afterward, Tomoya and Ushio visit Tomoya's father. Tomoya manages to convince his father into moving back to the countryside with his mother. While Tomoya and Ushio say goodbye to Tomoya's father, a 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 Fujibayashi and they have a conversation. After that, Tomoya goes to work and Yoshino asks him for Fuko to play with Ushio, since she likes her. Tomoya agrees to this and Fuko arrives at his house to play until the evening when she goes back home. When it is time to sleep, Tomoya uses Nagisa's song to lull Ushio to sleep. The next day, Kyou tells Tomoya about 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 with Sanae and Akio, when Ushio is suddenly struck with a fever, much to the others' shock.
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. Later, Fuko and her sister 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 begins there.
One year before the events of the beginning of the story, Tomoya is beginning his second year, and Nagisa her first time as a third-year student. Nagisa is having trouble making friends as usual, while Tomoya and Youhei are busy being delinquents and carrying out pranks at Kyou's, 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 first-year students, a classmate of Nagisa's finally finds the chance to talk with her and they become friends. Nagisa keeps the banner from the prank (with a message to instill confidence written by Tomoya), because she feels it attributed her to making 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, he begins to quite clearly recall a more tragic set of circumstances. 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.