Siblings Utsutsu and Yume Hasegawa are left alone by their abusive parents, relying solely on each other. However, their world is interjected by the appearance of stunning red butterflies. Unbeknownst to them, these beautiful creatures mark the onset of a horrifying virus, Pupa. Yume succumbs to the full effects of Pupa, transforming her into a monstrous creature with an insatiable hunger for flesh. In contrast, Utsutsu gains the ability to regenerate. Despite their differences, Utsutsu remains committed to his promise of protecting his beloved sister, even if it means sacrificing everything. Pupa follows the story of a brother's valiant efforts to rescue his sister from her hunger while safeguarding the world.