In order to help Fuko out, Tomoya and Nagisa take her to stay at Nagisa's house for the time being. Nagisa's family helps with carving more starfish out of wood, and at school Tomoya and Nagisa help with passing them out to students. Later, Fuko talks about how she has wanted to attend classes, but has never been able to. Tomoya makes arrangements with Youhei, Kyou, and Ryou to act as classmates in Fuko's very first high school class, and even Sanae comes to act as the teacher.

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.

It is now during summer vacation, but despite now having been going out for weeks, both Tomoya and Nagisa are still very nervous about it and have not done much to progress their relationship which comes as a shock to their friends. Mei comes back for another visit and after learning of Tomoya's and Nagisa's current stagnant relationship, decides to be their personal cupid of love in order to advance things along. Mei thinks up a whole plan which Nagisa attempts to follow despite it being very embarrassing for her at times. After Tomoya calls Mei out, she runs away, though Nagisa stops Tomoya from chasing after her. With some time left in the day, Tomoya and Nagisa take a walk together.

In an alternative timeline where Tomoya and Tomoyo are dating, Tomoyo becomes student council president, but bad rumors start around the school due to Tomoya's bad reputation. Tomoyo becomes busy during the school festival, and continues to be so while she attempts to save the sakura trees in town. Tomoya realizes that he is holding Tomoyo back from greater things, and despite both sides being reluctant, they break up. Time passes as Tomoyo's reputation builds and Tomoya and Youhei watch on the side through her many accomplishments, one of them being ultimately saving the sakura trees by the winter. At that time, Tomoya and Tomoyo meet and talk for the first time in months and they decide to become a couple again.

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.