After arresting Jessie Bains in Police Quest 1, Bonds is promoted to the homicide division. He begins dating Marie Wilkans, who helped him in his undercover work in exchange for the dismissal of prostitution charges against her. Their peaceful life is however short lived: When Bains is returned to Lytton for retrial, he manages to escape from prison, taking one of the guards as hostage using a makeshift knife.
Bonds and his partner Keith Robinson gather evidence at the jailhouse and locate the kidnapped jailer's car, when they are called to the riverside where Bains has apparently been spotted. Dodging a shootout with Bains, after which he escapes, Sonny soon dives and finds the body of the guard submerged in the river. Locating Bains' getaway vehicle near the Airport, Sonny investigates and finds out that Bains has since assumed the dead jailer's identity but still cannot determine Bains' next move. After going off-duty that evening, Bonds dates with Marie and they discuss the unfolding menace.
The following day, the body of Woody Roberts, a witness in Bains' trial (formerly the bartender at Hotel Delphoria in Police Quest 1) is discovered near the city's warehouse district. Evidence at the site directs Bonds and his partner to a motel in town, where the two storm Bains' room assisted by the local S.W.A.T. unit. While Bains himself is not present, Bonds finds a hit list on those that Bains intends to take revenge on who testified against him, including Bonds, Marie Wilkans, the already murdered Woody Roberts, and Don Colby, a former small time drug dealer now under the witness protection program. Hurrying to Marie's house, Bonds finds signs of struggle and clear indication that Marie has been abducted by Bains.
Bonds' detective work and the accumulated evidence lead him to believe that Bains has flown to Steelton where he intends to hit Don Colby. Alerting both Colby and the local police, Bonds and his partner take a flight there as well. On the way, they avert an attempted terrorist bombing of their plane. Arriving at Steelton, Bonds learns that Bains has already murdered Colby before the local police could react. A phonecall to Colby's office is traced to a local park, and Bonds heads there to investigate, quickly tracking Bains into the sewer system below the park. After navigating the dangerous sewers, Bonds finally confronts Bains in a shootout, during which Bains is shot dead, and Marie subsequently saved.
Depending on who shot first, the player can get two different endings. If Bonds shot first, then the jury will rule that he acted recklessly, and thus violated the law, giving the player the bad ending(Sonny loses his badge). If Bains shot first, then the jury will rule that he acted on self-defense, giving the player the good ending(Sonny is decorated by the department, takes off for the Bahamas with Marie, and proposes on the plane).By: binford6001