The story starts with a scene where Sanae was raised by her biological parents since her childhood, and her family had connections with the Moriya Shrine, where she occasionally visited. Everyone believed her to create miracles, but nobody knew about her bloodline with the gods, so she could talk with Kanako and Suwako telepathically and saw their bodies as if they were spirits. One day, many years after she grew up, she had to go to the Moriya Shrine alone for a festival where she would be the shrine maiden for that occasion, but she got a phone call from the police that her parents had died in a vehicle accident; both of them. She couldn't do much but cry by herself on the stage, hiding it from everyone. Everyone left the shrine because she couldn't perform on the stage due to her grief. Later, she was visited by Kanako and Suwako in their spirit form without her noticing while crying.
At the funeral, she stood near her parents' graves, crying, with other people standing behind her. She was also joined by Kanako and Suwako. At her house, she was visited by Kanako and Suwako after years, which caused her to remember them vividly. They invited her to Gensokyo, where they reestablished the Moriya Shrine once again. After that, she lived far away from the city she was born in, away from all the previous memories, to start a new life with the actual Kanako and Suwako in their physical form. Within the shrine, she still has a family photo with her parents, along with Kanako and Suwako, whom she now recognizes as her new parents. This was kept a secret until Kanako found it and later said to Suwako that they wouldn't raise this topic anymore.