Since there are one hundred per level, collecting bugs can get significantly more difficult than the items in Enter the Gecko. Unlike Enter the Gecko, when losing a life, Gex retains only the amount of bugs collected up to the latest checkpoint if the level has no checkpoint, Gex has to start from zero. He can spit fire and ice, as well as swim. There are also some aspects of the game that are shared only with the first installment, such as: Gex can only collect bugs in all levels (100 per level earns a remote) and secret levels, instead of the variety of items he collected in Enter the Gecko (skulls, TNT plungers, carrots, TVs, police plates, etc.). Gameplay remains similar to the previous game, Gex: Enter the Gecko, with the addition of certain vehicles, such as a tank, a camel and a snowboard, as well as a gliding ability available with certain costumes. With the help of his newly hired turtle butler Alfred and new friends Rex and Cuz, Gex manages to destroy Rez once again. Each level parodies a certain aspect of television culture (here the levels exist as stand-alone channels).

He teleports to the batcave-like lair he has in the Media Dimension, and begins another adventure. She then contacts him via his TV telling him that Rez has returned once more and has kidnapped her to get to Gex. When secret agent Gex is watching the news on his TV one day, he discovers that Agent Xtra (the agent from Gex: Enter the Gecko's backstory), head of the TV Terrorist Defense Unit, has been reported as missing.

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