In the winter of 1967, a 20-year-old man returns home from his travels aboard a ferry, where a chance encounter forever alters his perception of the world around him. While relaxing in the cabin, he is approached by a beautiful yet enigmatic girl who introduces herself as Emanon; later that evening, the pair accompany each other to dinner.

After seeing the man read a science fiction novel, Emanon offers to tell him her life story, saying that he doesn't have to believe it unless he wants to. And much to the man's surprise, she proceeds to inform him that her memory dates back over three billion years, to the very moment when life first appeared on Earth.

Omoide Emanon tells the extraordinary tale of a girl who serves as the planet's witness—an inheritor of genetic memory that has been passed down her maternal line since the beginning of life itself.