In the Nintendo 64 version most of the sexual references are gone due to Nintendo being a more family friendly game company. For example, in the cinema behind the blinds for the movie is a ufo, and the porn shop is changed to a comic shop.

In the original versions, the babes kidnapped by the aliens were woven into cocoons and tied up on pillars. Pressing the action button in front of them will make them moan "Kill me...", which is a reference to a similar scene in the Alien franchise. In the Nintendo 64 version, the babes were covered up more (as they were either naked or only had underwear on), and could not be killed (which is how you "saved" them before). The action button now makes the disappear and the message "Babe saved!" is shown.

In level 2-8, Lunar Apocalypse-Lunar Reactor, there is a reference to Star Wars Episode V: The Empire Strikes Back. You can find a dead Luke Skywalker hanging upside down at the back of a cavern. In the N64 version of the game, Luke is replaced with Yoda.