Perfect Dark Zero is set in the year 2020, three years prior to the events of the original game.Joanna Dark is a bounty hunter working with her father Jack and her friend Chandra. One day, they are commissioned to rescue an injured scientist named Zeigler from the hands of a Triad crime lord known as Killian. However, Zeigler is killed shortly after being rescued. Before dying, Zeigler used a neurodrive to implant information into Jack's mind in order to hide his valuable research.
While escaping from their enemy forces, Jack gets captured by a megacorporation known as dataDyne. On her next mission, Joanna is ordered to rescue him in a dataDyne facility located in a mountainous region of China, but Jack eventually dies at the hands of Mai-Hem, whose father, Zhang Li, is dataDyne's founder. Alone with only Chandra looking out for her, Joanna is then sent on a mission to find Dr. Eustace Caroll, who then uses the same neurodrive technology to extract any memory of the words her father said to her concerning Ziegler's secrets. Dr. Caroll is then killed by Chandra, who was secretly employed by dataDyne. Nevertheless, Joanna is suddenly rescued by agents from an agency known as Carrington Institute, whom she agrees to join in order to stop dataDyne.
Zhang Li and Mai-Hem are searching for an ancient artifact, which acts as a power-source for the Graal, a device which endows individuals with superhuman powers, hinted to have been built by the Maians, extraterrestrials encountered in the original Perfect Dark. Travelling to Africa, Joanna rescues prisoners including Jonathan Steinberg, a veteran agent of the Carrington Institute, and several other Carrington soldiers, before running into Mai-Hem again. Joanna avenges her father's death and kills Mai-Hem and the party is air-lifted out. The Carrington Institute plans an offensive on dataDyne forces with the battle taking place on a large bridge. Joanna infiltrates an arena and faces off against Zhang Li, on the Graal after he dispatches Chandra. Defeating the seemingly invincible power-hungry genius, Joanna is met by Jonathan and Carrington Institute founder Daniel Carrington. When Joanna asks, "How did I do, boss?" Carrington replies, "Perfect."