Perfect Dark is set in 2023 against the backdrop of an interstellar war between two races: the Maians, who resemble the archetypal grey alien, and the Skedar, reptile-like extraterrestrials who use a holographic disguise to appear as Scandinavian humans, bearing similarities to Nordic aliens. Using this disguise, they can interact with humans on Earth without looking too overtly suspicious. Meanwhile, on Earth, there is an ongoing rivalry between two factions: The Carrington Institute, a research and development center founded by Daniel Carrington that secretly operates an espionage group in league with the Maians; and dataDyne, a defence contractor corporation headed by Cassandra De Vries that secretly maintains a deal with the Skedar: in exchange for creating an AI capable of cracking an ancient alien spacecraft buried on the ocean floor, the Skedar have agreed to supply them with enough alien technology to become the biggest corporation on Earth.

Perfect Dark Zero is set in 2020 where a large percentage of the world is controlled by corporations. The most notable of these corporations are dataDyne, headed by Zhang Li, and the Carrington Institute, headed by Daniel Carrington. The player is cast as Joanna Dark, a bounty hunter working with her father Jack Dark and computer hacker Chandra Sekhar. The team is after Nathan Zeigler, an independent researcher who has been captured by a Hong Kong triad gang led by a man named Killian. Joanna and her father successfully rescue Zeigler, but Killian manages to escape. Zeigler explains that Killian was trying to obtain his research, which contains information about a dangerous weapon. As Zeigler refuses to go anywhere without his research, Joanna is sent to retrieve it while her father stays with Zeigler. After Joanna retrieved a case with Zeigler's research from a nearby safe house, Zeigler takes a device called neurodrive from the case and uses it to implant his research data into Jack's mind. Afterwards, Zeigler succumbs to his injuries sustained by Killian and dies. Before dying, Zeigler says that they must find a scientist named Dr. Eustace Caroll.