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

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

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

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

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

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

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

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

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

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

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

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 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

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 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

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

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

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

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

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

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

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