Kotomi returns the violin to Rie Nishina and becomes friends with her. Kotomi changes her usual routine and starts attending her classes. Due to Kyou's idea, she, Ryou, Kotomi, Nagisa, and Tomoya go out together as a group and have fun in town. While out, Fuko makes an appearance in, but no one remembers her. The next day, Nagisa runs up to Kyou thinking Ryou got in a bus accident, though when they rush to the scene, they find no one was hurt; however, Kotomi has an emotional episode and collapses while screaming out. Kotomi leaves early that day, but when Tomoya, Nagisa and the Fujibayashi twins go to see her later, there is no answer at her house. After they leave, Tomoya goes back and runs into the strange man from earlier; he finds out the man is an acquaintance of Kotomi's parents.

Tomoya realizes that he met Kotomi as a kid, though only she had remembered. Back then, Tomoya had often visited Kotomi, and was her only friend. Around this time on Kotomi's birthday, her parents left for business reasons, and later that day she finds out they were killed in a plane crash. Kotomi ultimately ended up burning her father's important work before anyone could see it. While Kotomi shuts herself in her house, Tomoya comes over and starts cleaning up the garden which is overgrown with grass and weeds. Nagisa, Kyou and Ryou eventually help out too.

Kotomi finally leaves the house to find that Tomoya worked in the garden all night long and had fallen asleep. When she returns to school, Tomoya, Kyou, Ryou and Nagisa are all waiting for her. The mysterious stranger whom she was so frightened of, believing he wanted to steal her parents' thesis, is there as well. Kotomi and her friends find out that he is her legal guardian, and that there never were any written notes for the thesis after all. The envelope Kotomi set fire to, and felt so guilty about, was nothing important. The stranger also has a birthday gift for her: her parents' suitcase, which survived the plane crash and was passed from hand to hand for years until he found it. Inside is a teddy bear, Kotomi's gift request to them before they left, and an affectionate letter. Kotomi, holding the bear, is so happy that sparkles literally fill the room, and makes peace with her parents' deaths at last.

Tomoya, Nagisa, and Youhei finally find out that Yukine is respected by the two rival gangs in the city since she helps both sides' members after they get hurt. Her older brother is the leader of one of the gangs, and a young boy named Yu comes to her to find his older sister who apparently is dating a guy in Yukine's brother's gang. Youhei tells Yu that he is Yukine's brother for a time, but the truth is later revealed after Yukine takes Yu, along with Tomoya, Nagisa, and Youhei, to a bar where her brother's gang hangs out. Yukine's brother has been in the hospital since he saved a friend and got in a car accident. While heading home, three members of the rival gang think Youhei is Yukine's brother and try to fight him and Tomoya, but Tomoyo intervenes, stopping them single-handedly.