Three years after "the event" in New York, Aya Brea has joined the FBI to help control the threat of another mitochondria outbreak. After encountering several Neo Mitochondrial Creatures (NMCs) in a Los Angeles office building, Aya starts on an investigation into the source of the situation. She will have to travel to a variety of locations and fight dozens of NMCs that don't want her to discover the truth behind their existence. Luckily, Aya is trained in the use of several weapons including pistols, rifles, and machine guns. But when things get a little too hairy, she can call on the power of her own mitochondria and pull off special attacks or heal wounds. Your performance throughout the game determines which of the multiple ending you will get to see. It's up to you to try to keep the mitochondria in check with PARASITE EVE II.