Shortly after the fall of STAG, Pierce, Shaundi and the Boss are called upon to assist MI-6 agent Asha Odekar and her contact, former Deckers leader Matt Miller, in infiltrating a Middle Eastern compound to assassinate Cyrus Temple, the former leader of STAG who has since gone insane and obsessed with killing the Saints leader when his plan to frame the explosion of a statue on the saints is ruined, and plans on destroying Washington, D.C. using a nuclear missile. The Boss manages to kill Cyrus, but is unable to stop him from launching the missile. Climbing aboard the missile, the Boss disarms the nuke in midair before it reaches Washington, earning the adoration of America.
Five years later, the Boss has been elected President of the United States, with several members of the Saints acting as cabinet. While preparing for a press conference, the Boss is told that Asha and Matt have arrived at the White House, which the Saints have renamed the White Crib, to warn them of what they suspect is an impending alien invasion. Just as the Boss is informed, the invasion begins, spearheaded by the alien warlord Zinyak, who captures all of the cabinet members as well as the Boss.
The Boss wakes up in what appears to be a 50s sitcom set in the city of Steelport, devoid of violence or foul language. The Saints' computer hacking specialist, Kinzie Kensington, contacts the Boss and informs them that they are trapped inside a simulation, and that each of the Zin's prisoners are trapped in personal simulations of their own fears in order to break their will, as the Boss fears a world of utter conformity. With Kinzie's help, the Boss breaks free of the simulation and joins Kinzie and Vice President Keith David in a stolen Zin ship. While the trio attempt to contact reinforcements from Earth, Zinyak atomizes the planet, killing everyone not already captured by the Zin. Determined to get revenge for Earth, the Boss returns to the Steelport simulation, hoping to use it to find the