Kanon's story, set in the middle of winter, regards a group of five girls who are connected back to the same boy. Yuichi Aizawa, the main protagonist, had visited the city where the story takes place seven years prior to the story's beginning.

In the beginning Yuichi is very detached from the city and its inhabitants. Prior to his return, it is decided that he is to stay with his cousin, Nayuki Minase, and her mother, Akiko. After his long absence, Yuichi has forgotten almost everything except minor details of what happened seven years before and is in need of being reminded of what he left behind.

On the day after Yuichi's return, he is out with Nayuki who is showing him around town. Nayuki remembers that she has to buy things for dinner and Yuichi is reluctant to go with her, arguing that he might get lost. Moments after Nayuki left him waiting on the sidewalk, a strange girl named Ayu Tsukimiya barges into him with little warning. Upon recovering, she drags him away to a nearby café and confesses to inadvertently stealing a bag filled with taiyaki after being accidentally scared away by the salesman before she had a chance to pay. Yuichi then drags Ayu back to the salesman, they both apologize for the trouble, and Ayu is forgiven. They decide to meet up again another day and Ayu scampers off.

Yuichi is not aware at first, but three other girls which he had forgotten are familiar with him. Throughout the story, as he learns about the supernatural undertones of the town, Yuichi is reminded of each girl and the events of seven years ago in the city covered in snow.