The player assumes the role of Hunter, a computer expert who is hired by the Johnston Biotek corporation, referred to as the "Corporation" in the game. Hunter is to repair the network of a mining complex but fails and ends up in an underground cave world after an explosion. A man called Toadstool finds him and tells him where he is: In an underground world where a computer freak called Hacker has seized power. Left alone by the Corporation, Hunter has to find a way back to the surface all by himself. On his quest he meets Kathryn, a mysterious woman, who sometimes helps the player. Hunter faces many dangers and problems; for instance, when he is confronted by sinister figures in an underground prison colony.

After the happenings of Saints Row: The Third, the Saints gang extended their reach and the protagonist became the President of the USA. Unfortunately during a press conference, disaster happens: aliens attack the White House, kidnap the Saints and trap each in their personal, indefinitely looping nightmare. Fortunately Kinzie, the group's hacker, rescues the protagonist and together they flee into a space ship with the goal to rescue the rest of the gang. The majority of the game it spent in an open world simulation of Steelport, the location of Saints Row: The Third. There is an extensive character creation which allows to tune every aspect of the protagonist's look and the choice between seven voices (three male, three female and Nolan North).