Lake Yomi tells the story of a 13-year-old girl, Nozomi, who struggles to cope with the death of her mother. While helplessly battling against the unfairness of fate, she unexpectedly finds herself deep-diving into Lake Yomi; a sacred lake infamous for its tales and lore. There, she meets Mizuha, a foreign being who claimed the lake as her home. But after waking up dazed and confused in her bed, her late mother suddenly appears in her life once again. Nozomi is faced with a choice, one that would rewrite her fate and that of the people around her forever.