Anna, a young girl living in Sapporo, is having trouble with her classmates. Due to asthma attacks, a doctor suggests that Anna move somewhere more relaxing. After moving to the countryside to her family, separated from her mother, she spends her time walking around the area and sketching. She finds herself drawn to a seemingly abandoned house across the water, which can only be walked to during low tide. It is there that she meets Marnie.

Although she finds Marnie to be the first kid her age that she gets along with, there is something mysterious about her—Marnie even tells Anna to keep her a secret from the town. Anna has trouble remembering things, and even blacks out. How are these things related to Marnie? Just who is this strange girl?