Twelve years after he saved the Earth from an alien invasion, Duke Nukem has become a celebrity multimillionaire. After playing a game based on Duke Nukem 3D, he arrives on the set of a talk show for an interview. On his way to the show, Duke witnesses a news broadcast announcing that aliens have returned.

Unlike previous encounters, the aliens initially appear peaceful and at first seem to pose no harm to the humans of Earth. Duke's talk show appearance is cancelled to allow television stations to cover the alien invasion, so Duke retires to the Duke Cave.

There, he receives a call from the president and General Graves of the military. The president orders him not to harm the invaders, and he adds that he is in diplomatic talks with the alien overlord.

Duke obliges this request but remains uneasy. Before Duke can leave his chambers, he is attacked by hostile aliens. Duke is forced to disobey the president's orders and fight his way through the alien hordes in an effort to save Earth.

While fighting through his Las Vegas casino, Duke witnesses the aliens abducting women, including his two pop-star girlfriends.