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.

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.

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.