After the unexpected death of her father, 11-year-old Momo Miyaura leaves Tokyo with her mother and moves to an old remote island in Seto Inland Sea. The only memento she has from her father is an unfinished letter with only two words inside: "Dear Momo"—along with her heart's unrest from it. In the new and unfamiliar small town, Momo reluctantly tries to adjust to the outmoded wooden buildings, silent crop fields, and mysterious isolated shrines. One day, while exploring the attic of her new home, she finds a worn out picture book about youkai. Following this discovery, strange things begin to happen around town, and Momo is greeted by the arrival of three troublesome youkai. Momo e no Tegami tells the story of a young girl as she struggles to adapt to her bizarre new life and ultimately come to terms with her father's mysterious letter.

In 1945, World War II is at its peak. As Japanese cities are fire-bombed and the nation is cornered by US forces, Japan is collapsing under the immense pressure. Gen Nakaoka, a bold, free-spirited young boy, lives in Hiroshima. Struggling with wartime scarcity and barely making ends meet, Gen and his family are hopeful that the conflict will soon end with Japan's imminent defeat and their city unscathed. However, unbeknownst to them, their fate is already sealed with the impending dropping of "Little Boy," the US atomic bomb set to cause the devastating cataclysm that will forever change Japanese society.

In an attempt to turn his floundering career around by compiling one hundred ghost stories, struggling author Momosuke Yamaoka roams through Edo-period Japan searching for material. During his travels, the young man wanders deep into the mountains, where he encounters a monk named Mataichi. Failing to heed the monk's advice to turn back, Momosuke presses forward and soon witnesses a murder carried out by Mataichi and his two associates. As it turns out, Mataichi's gang also investigates paranormal incidents—aiming to make those in the wrong pay the ultimate price. Continuing to seek out subject matter for his stories, Momosuke repeatedly crosses paths with the trio of outlaws, becoming increasingly involved in their schemes each time. As the author strays further toward the world of darkness, he grapples with both the morality of the group's actions and the line between humans and the supernatural.