At the end of Saints Row, the protagonist was aboard Alderman Richard Hughes' luxury yacht when a bomb exploded on the yacht leaving the fates of Hughes and the protagonist unknown. In Saints Row 2, it is revealed that Hughes was killed and the protagonist was put into a coma. Five years pass and the protagonist awakes in a prison hospital ward and received extensive plastic surgery. The protagonist meets inmate Carlos Mendoza and the pair escape the island and return to the protagonist's home city Stilwater, rebuilt by the Ultor Corporation after a devastating earthquake that left parts of the city below sea-level. The protagonist then rescues his/her friend Johnny Gat from a courtroom proceeding, enlists the help of Carlos, Shaundi (a former college student and bohemian), and Pierce Washington (the gang's new strategist), and begins to rebuild the divided Third Street Saints gang.[23] The protagonist, now referred to as the Boss for most of the game, leads the Saints on a quest to retake the city. The main storyline is divided into three separate story mission arcs, completable at any time and in any order.
The Boss and Carlos meet with Maero, leader of the Brotherhood of Stilwater in the Underground Caverns. However, police discover the meeting and the three are forced to shoot their way to safety. Despite working together aganist the police, the Boss becomes enraged at Maero's offer of a 20/80 split of profits between the Saints and the Brotherhood. This sparks a feud between the Saints and the Brotherhood, and the Boss shakes Brotherhood mechanic Donnie, a former Westside Roller (a rival gang from the first Saints Row) to rig the gang's truck and also burns Maero's face by poisoning his tattoo ink with radioactive waste. The Brotherhood retaliate by kidnapping and brutally torturing Carlos by dragging him behind a truck, forcing the Boss to end his suffering with a mercy kill. The Boss exacts revenge by kidnapping Maero's girlfriend Jessica, and arranges for her to be inadvertently killed by Maero in a monster truck rally. After interrogating and crippling Maero's tattoo artist Matt at a concert, the Boss begins to uncover information about the large weapons shipment. Maero angrily confronts Dane Vogel (voice of Jay Mohr), CEO of the Ultor Corporation, demanding the release of arrested Brotherhood members with Chief Of Police Troy Bradshaw. Although freed, the prisoners' buses are intercepted and destroyed by the Saints. Maero kicks in the door to Vogel's office intending to threaten him again, but finds himself confronted by a heavily armed team of Ultor security guards. Vogel dismisses Maero, calmly informing him that the weapons shipment the Brotherhood was expecting will be seized by Ultor as "payment" for Vogel's arranging the release of the imprisoned Brotherhood members. The Boss intercepts the shipment and launches an attack on the crippled Brotherhood's hideout. After the Saints fight their way through Brotherhood gang members, Maero ambushes the Boss with a minigun on the roof of a warehouse. After running out of ammunition, Maero hurls his minigun at the Boss and the two fight hand to hand, eventually crashing through to the ground floor of the warehouse. Just as the Protagonist is about to finish Maero, Matt sacrifices himself by forcing the Boss off Maero. The Boss quickly kills Matt, but Maero manages a narrow escape from the Saints when Donnie arrives in his truck. Maero then challenges the Boss to a final face-off at the arena with him and his men in trucks, but loses the fight and is shot in the head by the Boss, with his last words being "Go to hell."
Shaundi begins to gather information on the Haitian Sons of Samedi gang, and learns of their illegal drug trade. The Saints then target various assets in the production of the 'Loa Dust' drug. Gang leaders, the General and Mr. Sunshine, order their lieutenant Veteran Child to kill his former girlfriend Shaundi, who had passed the information. Although he succeeds in kidnapping her, the Boss kills him and saves her. The General then kidnaps and drugs the Boss and orders an attack on the Saints, but the Boss escapes and the Saints are able to hold off the attack. Through tips from an addict, the Boss uncovers Mr. Sunshine's hiding place, a meat-packing plant, and the Boss kills him there, decapitating him and tossing his head along with an assembly line. The Saints then co-ordinate an attack on the General's convoy and kill him in the mall as he flees.
As Johnny and Pierce assist the Boss to take down the Japanese Ronin gang, they decide to rob a Ronin owned casino. However, they end up stealing money from Ultor, who are under Ronin protection, and Vogel demands that action be taken against the Saints. Leader Shogo Akuji orders an attack on Johnny and his girlfriend, retired R&B singer Aisha, the result is Aisha sacrificing her own life to warn Gat of an ambush, and Ronin second-in-command Jyunichi stabbing Johnny Gat, hospitalizing him. Shogo's father and international Ronin leader Kazuo Akuji arrives in Stilwater and takes over, demoting Shogo to lieutenant. After Jyunichi is killed in a sword fight face-off with the boss and the Ronin's hotel is hit, Kazuo disowns his son and shows regret at giving him power over the Ronin. At Aisha's funeral, Shogo attacks Johnny and the Boss but is buried alive after being captured. Kazuo threatens the Boss' longtime friend and leader of the Triads gang, Mr. Wong and is killed by the Boss during a Chinese New Year's celebration, being burned to death.
In the aftermath, Dane Vogel uses the Saints' overthrow of the city to stage a coup d'état within Ultor, tricking the Boss into killing the rest of the board. However, when Vogel attempts to take control of Ultor, the Saints stage an assassination attempt at a press conference. After fleeing to safety in the Philips Building, Vogel is met face-to-face by the Boss, who shoots him in the mouth, killing him instantly, crippling the Ultor Corporation and ensuring the city under the Saints' control. Wiretap conversations reveal that one of the surviving members of the old Saints, Dexter Jackson took up a job offer with Ultor, and that former Saints' leader Julius Little planted the bomb from the original game's climax hoping to kill the Boss and let the Saints dissolve, through threats from undercover cop Troy Bradshaw. A mission becomes available and the Boss contacts Dex, who tells the Boss to meet him at the old Saints' church. Upon arrival, the Boss finds Julius, who was also told by Dex to meet there. The two are ambushed by the Ultor Masako Team and are forced to flee. Julius and the Boss drive around the city while being chased by Masako APCs, until they crash in the Amphitheater. The Boss then shoots Julius in the chest. Shocked, Julius explains that the Saints never solved a thing, having become the same as the gangs they had been fighting. The Boss then takes revenge by shooting Julius in the head.
Ultor microbiologist Tera Patrick meets with the Boss at the Saints Hideout and reveals that she knows some of the Ultor Corporation's dark secrets. The Protagonist, not wanting to pass the chance of exposing Ultor, agrees to help Tera out. The Boss digs up the bodies of discarded test subjects (The discarded bodies look like the zombies from the Saints Row 2 diversion Zombie Uprising) from a nanorobotics experiment as evidence. However, the press refuses to run the story and so the two hijack a truck containing chemicals that Ultor used in the experiments. News reporter Jane Valderamma is met by the Boss and says that she wants an interview with Tera if she is going to run the story. Tera, who fears being on live TV, begrudgingly agrees and when the microbiologist is interviewed, Jane deliberately turns the interview on Tera after she tells that she was the one who conducted the experiments. After the interview, Tera promises Jane that she will find a way to expose Ultor, even without her.
CEO of the Ultor Corporation and successor to Dane Vogel, Eric Gryphon requests protection from the 3rd Street Saints in exchange for information on Dexter Jackson, an original lieutenant for the Saints (See Saint's Row) who now works as the Ultor Corporation's head of security. After meeting with the Boss at the Saints Hideout, Eric meets with Dex saying that he is unafraid of Dex's attempts to kill him. Eric reveals to the Boss that Dex has been selling nuclear waste on the black market and is using the Ultor Masako Team to cover up the evidence. The Boss then steals the waste from the nuclear power plant for himself, crippling Dex's finances. Dex abandons his position in Stilwater and requests a job transfer, fleeing to another city. The Boss learns of this through Eric, who in turn helps the Boss eliminate key associates of Dex during the Ultor Family Picnic. The Boss then reveals to Eric that he will find out which city Dex fled to and kill him, a hint about a possible sequel.
And then Saints Row 3 happened
