 Following the climactic battle at the end of Space Quest 5, starship captain Roger Wilco is charged by the Confederation with causing the destruction, and is demoted back to his old-time post of janitor, and assigned to active duty aboard the starship Deepship-86. While on shore leave on the seamy planet Polysorbate 60, Roger is targeted by a mysterious evil mastermind as an appropriate tool for a nanotechnology life-prolonging experiment. But when several attempts to kidnap Roger are foiled by his lovely female shipmate Stellar, the mastermind decides to use her instead of Roger. The hapless Roger must now set out alone to find Stellar and, in miniaturized form, to infiltrate her body and do battle with the robotic mastermind who is taking over it.