Saints Row IV is the game takes place years after the events of its predecessor, in a virtual reality based on the fictional city of Steelport, in which the protagonist must fight an alien invasion as well as simulations of the gangs and enemies from their past.
The game's plot sees invading aliens placing the player in to a computer-simulated version of Steelport early on, and the bulk of the game takes place within this simulation. The simulation has Steelport constantly cloaked in the darkness of night, with largely computer-themed twists on classic Saints Row elements. Objectives are often based around hacking the simulation in order to work towards escaping it.
The Boss wakes up in what appears to be a 50s sitcom set in the city of Steelport, devoid of violence and 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 try 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 make use of it to find the remaining Saints and somehow reach Zinyak. The Boss begins to go in to the other Saint's simulations in order to rescue them, revealing each of their own fears including Matt's fear of being trapped in the cyberworld and Killbane coming after him, Shaundi's fear of her former calm and fun-loving self, Pierce's fear of the Saint's picture turning on him, Benjamin King's fear of his former gang the Vice Kings, and Asha's fear of failing an important mission.
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Soon after the fall of STAG, Pierce, Shaundi and the Boss are called on 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 designs on destroying Washington, D.C. using a nuclear missile. The Boss manages to kill Cyrus, but is unable to cease him from launching the missile. Climbing aboard the missile, the Boss disarms the nuke in midair before it reaches Washington, earning the adoration of The united states.
Years later, the Boss has been chosen 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 imminent alien invasion. 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.
Matt Miller, having abandoned the Deckers and, according to news broadcasts in Saints Row: The Third, announced an abstinence from the use of expertise, presumably returned to the United Kingdom and became employed by MI-6 alongside new character Asha Odekar. Johnny Gat also returns after being thought dead in Saints Row: The Third. Stilwater, the location of the first games, makes an appearance for mission with most of the street gangs from the first games making appearances as well.
A number of characters from earlier games in the franchise - both members of the Third Street Saints and former adversaries - make a return in Saints Row IV, lots of of whom take up the protagonist's Presidential administration. Kinzie Kensington, the socially awkward FBI hacker from Saints Row: The Third becomes the White House's press secretary, often tasked with clearing up the mess left behind by the President's verbal missteps. Benjamin King, former leader of the Vice Kings gang from the original Saints Row, becomes the President's Chief of Staff, while Pierce Washington has been appointed the Communications Director and Shaundi as the Director of the Secret Service.