In the second part of the story, which starts immediately after the end of the first part but extends into the next ten years, Tomoya and Nagisa live together as a family. Tomoya has to endure several hardships that the family has been suffering from, mainly involving Nagisa's illness. Just after Nagisa gives birth to their daughter Ushio, Nagisa dies, leaving Tomoya to fall into a state of depression. This causes Nagisa's parents, Akio and Sanae to look after Ushio. Five years later, Tomoya meets Shino Okazaki, his grandmother on his father's side. Shino explains to Tomoya about his father's past and tragedy, similar to Tomoya's current situation after Nagisa's death. After hearing that, Tomoya decides to raise Ushio and acknowledge Naoyuki as his father. Shortly after Tomoya regains his purpose for living, Ushio is struck with the same disease as Nagisa. Tomoya, Sanae and Akio struggle to save Ushio, with Tomoya retiring from his job, but all efforts are futile. In the coming winter, wanting to do anything for Ushio, Tomoya decides to take Ushio on a trip, but Ushio falls unconscious and dies shortly after.
Tomoya's psychology developed in his dreams of a bleak world where small orbs of light float around called the Illusionary World (幻想世界, Gensō Sekai?). In the first few dreams, he sees a world devoid of all life except for one girl (and grass). Each time he dreams, he finds out more about the world. Tomoya discovers the girl has a special ability to fuse junk together to create new things, with which she creates a body for him. Thus he is reborn in this world, and fills time following the girl around. Tomoya conceives that only the two of them are "alive". To pass time, Tomoya and the girl try to build another doll with more junk they find, but as it has no soul, it fails to come to life. Remembering a distant world where he came from, Tomoya convinces the girl to build a ship so that the two can escape the approaching winter and continue a happy life. Eventually, winter sets in, and the girl becomes cold to the point where she cannot move any more. Upon meeting this tragedy, the girl tells Tomoya that he has another chance to go back and make things right. To do so, he must collect certain "lights" (symbols of happiness) similar to those floating around in the Illusionary World. If all the "lights" are collected throughout both story parts, a chance to save Nagisa from dying in childbirth will become available, and the true ending where Nagisa survives and lives with Tomoya and their daughter Ushio will also become available.