Parasite Eve is a horror RPG that follows the story of NYPD rookie Aya Brea. On the night of an opera performance in Manhattan, a singer named Melissa undergoes a drastic and horrifying transformation, causing a fire that kills most of the audience. Aya, who was attending the performance, witnesses the incident and discovers that Melissa's transformation is related to a phenomenon known as mitochondria.

As the story unfolds, Aya becomes entangled in a battle against Eve, a being born from Melissa's mitochondria. Eve is determined to wipe out humanity and create a new dominant species, and Aya must stop her before it's too late. Along the way, Aya discovers the truth about her own unique physiology and her connection to the mitochondria. With the help of scientist Kunihiko Maeda and NYPD detective Daniel Dollis, Aya battles through a series of encounters with Eve and her monstrous minions in order to prevent the end of humanity.

The game is set over the course of six days, each day presenting new challenges and revelations for Aya as she battles to stop Eve's plan. As Aya progresses, she gains new powers and abilities, unlocking the potential of her own mitochondria and becoming stronger and more formidable. Ultimately, Aya must face Eve in a final showdown, with the fate of the world hanging in the balance.