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.

More people from school are not able to see Fuko anymore and now even those close to Fuko in the past are beginning to forget about her. First Youhei forget after he goes to see her in the hospital, followed by Kyou and Ryou. Tomoyo manages to remember with Tomoya's help however. Later, Youhei manages to remember Fuko for a moment, but is unable to remember any more. Tomoya and Nagisa buy Fuko a birthday party set to cheer her up. When they get back to the bakery, they discover that Nagisa's father has forgotten Fuko, and while Nagisa's mother has not forgotten completely, she cannot see her anymore. Tomoya and Nagisa decide to take Fuko back to school for now.

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.

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.