There is little story in the game, only a brief text prelude located under "Help" in the Main Menu, and a few cutscenes after the completion of an episode. The game picks up right after the events of Duke Nukem II, with Duke returning to Earth in his space cruiser. As Duke descends on Los Angeles in hopes of taking a vacation, his ship is shot down by unknown hostiles. While sending a distress signal, Duke learns that aliens are attacking Los Angeles and have mutated the LAPD. With his vacation plans now ruined, Duke hits the "eject" button, and vows to do whatever it takes to stop the alien invasion.