The story unfolds as Daxter searches for Jak, who was imprisoned during the events that led to the start of Jak II. Daxter, now on his own in an unfamiliar place, quickly realizes that being small and furry won't help his chances of survival. To help stamp out a mysterious metalbug infestation, Daxter takes on a job as a pest exterminator, enabling him to explore parts of Haven City in an effort to collect the clues that will lead him to Jak.