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.

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.