The opening cinematic shows Riddick in hiding, having grown out his hair and beard, before the opening scene of the Chronicles of Riddick movie. He hunts an animal and after killing it, a disembodied voice starts talking to him asking him where he got his eyes. He states that he received them from a "slam preacher" and this causes him to remember his time at Butcher Bay. The game takes place in a flashback.
Another opening cinematic takes place in which Riddick is being transported for collection on the bounty. He and Johns have a brief conversation in which Riddick tells Johns that there is no way he is going to get the price he wants. Riddick wakes up as they land and stands out front of Butcher Bay waiting for the warden. He sneaks up behind Johns and breaks his neck and proceeds to escape. After getting his hands on a gun, he goes through the ventilation ducts and seemingly escapes into the desert. Everything fades to white as Riddick hears Johns saying "Rise and shine, Riddick." It turns out this escape was simply a dream.
Riddick wakes up and Johns escorts him off the ship. Johns meets with Hoxie to negotiate his pay,[12] while Abbott escorts Riddick to his cell in the "single-max" security area. After making enemies with and killing a gang leader named Rust, Riddick familiarizes himself with the facility, and soon instigates a riot; during the confusion, he escapes into the prison's sewer system. Armed with a shotgun and a dying flashlight, Riddick discovers he is not alone in the sewers. Fighting through the sewers against mutant "dwellers",[13] Riddick eventually meets Pope Joe, for whom he retrieves a lost radio, which Joe calls a blessed voicebox. A woman named Shirah (Kristin Lehman)[16] tells Riddick that he "has been blind too long", and he gains his trademark "eyeshine" night vision.[8] Afterwards, he accuses Pope Joe of tampering with his eyes; Joe says that he merely treated Riddick's injured arm. Riddick then continues his escape, while using the eyeshine to his advantage.
After emerging from a manhole in the showers of the guard living quarters, Riddick uses a guard uniform to blend in as he makes his way to the space port and his chance at escape. Realizing he requires a guard to get through the retinal scanner that locks the doors to the space port, Riddick decides to go after Abbott and take his eyes. He gains access to Abbott's apartment by telling him there is a delivery for him. A fire fight ensues and after that, as Abbott bleeds out on the floor, Riddick moves in for the kill but is stopped by Johns.
Riddick is captured and transferred to the "double-max" security area. Gaining the trust of the inmates by participating in fighting matches, Riddick eventually kills the champion of the fighting matches, a guard named Bam. This leads him to be taken to a room where no surveillance is seen and several guards await to kill Riddick. Abbott walks into the room, fully healed, holding a baseball bat. Shirah returns to him and tells him that the fury of all of his kind is within him, and he can release it if he chooses. A blast of energy called the 'Rage of Furya' kills all the guards around him except Abbott, who hides and then panics and attacks Riddick. Riddick kills Abbott and proceeds to find another way to escape. Using a secret entrance to an elevator, he infiltrates a mining facility. He meets an inmate of great influence in the area named Jagger Valance (Ron Perlman),[16] who wishes to escape with him. He makes a bomb and plants it in a mining site with a massive gas leak. However, Riddick is discovered and caught by the guards. During his transfer to another section, the prison is disrupted by an outbreak of creatures called "Xeno", due to the bomb Riddick planted, in order to create the confusion necessary for his escape, and Riddick attempts to escape with Valance. His plans are foiled again by Johns. After a fist fight, Riddick and Johns are both shot by Valance (who only meant to hit Johns) and Valance is killed by the guards. After meeting again with the warden, and telling him that he is just getting started, Riddick is placed in the "triple-max" area, where inmates are kept in cryonic sleep.[11] They are awakened daily for two minutes of exercise; during this time, Riddick discovers a flaw in the system and escapes. He then hijacks a large robot and fights his way through Butcher Bay to reach Hoxie.[17]
Tired of dealing with the prison officials, Johns helps Riddick to elude the guards. Riddick knocks Johns out and flies the ship into the warden's office. The warden calls in two robot guards with cloaking abilities and Riddick defeats them. After Hoxie surrenders, Riddick receives the codes to Hoxie's ship and Riddick and Johns escape disguised as a guard and prisoner. Two guards enter Hoxie's room, where Hoxie is bound and covered in Riddick's former attire. They mistake him for Riddick and kill him. Riddick and Johns take off in Hoxie's ship, ending the game.