Gex 3D: Enter the Gecko is a 3D platform game where the player controls a gecko who has to navigate several levels, all of which are parodies on well-known TV shows and movies, such as Looney Tunes, Gilligan's Island, or Friday the 13th.

Rez, the evil overlord of the television is back into the Media Dimension, and the government asks the TV addict gecko, Gex, to defeat him once again. He gets a lot of money and an agent suit for that. The game generally resolves around a James Bondish spy theme, but the story is not referenced later in the game.

Gex has to enter levels through TVs to collect three types of remote controls in order to unlock more of the Media Dimension, boss levels and secret TVs. Gex can tailwhip or karate-kick his enemies, climb certain walls and ceilings, eat bugs for power-ups, and spout one-liner wisecrack jokes. The gameplay is non-linear, the player can choose from multiple routes and goals on each level, and are replayable anytime after accomplished.