The game picks up where Escape from Butcher Bay left off.
Richard B. Riddick is a dangerous space criminal who can see in the dark. Johns, the man who originally took Riddick to the Butcher Bay prison for a bounty, helped him escape to avoid becoming a prisoner himself. On their ship together in a cryogenic sleep, they are dragged unwillingly into the Dark Athena, a gigantic mercenary vessel run by Gale Revas and her second in command, Spinner.
Riddick avoids capture as Revas and her men take Johns away. Using the same stealth tactics as he did in Butcher Bay, Riddick sneaks and hides throughout the ship seeking to escape, killing the guards and mercenaries he encounters along the way. Many of the guards are automated drones that are human bodies with implanted machine parts, controlled remotely from within the ship.