The game begins with Roger Wilco being court martialed for various humorous reasons (all of which Roger, being the idiot that he is, cannot defend properly). He is demoted back to his position as second class janitor aboard the SCS DeepShip 86 (a parody of "Deep Space 9"). Among the reasons for Roger being simply demoted and not expelled from StarCon is the "safe return of the SCS "Eureka"". This is a continuity error in that the "Eureka" was in fact destroyed in "Space Quest V".