Five years after the explosion on Alderman Richard Hughes' yacht, the player, who fell into a coma, awakens in Stilwater's maximum security prison after undergoing extensive plastic surgery. Carlos Mendoza, the brother of a former Saint, infiltrates the infirmary and helps the player escape. Carlos then informs the player about the demise of the 3rd Street Saints; Julius went missing, Troy Bradshaw became the Chief of Police, and the remaining Saints members were either killed or jailed. Arriving at a bar, the player discovers that Johnny Gat has been sentenced to death for 387 murders, and breaks into the courtroom to rescue him. The two then begin to revive the Saints, using an abandoned church as their new headquarters and soon recruiting high-ranking lieutenants in Carlos, Pierce Washington and Shaundi. The player then becomes the new leader of the Saints, being referred to as "the Boss".
