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, the later ability having not been present in previous games.

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 swimming ability and a gliding ability available with certain disguises depending on the level. Alfred informs the player that it was because of Alfred that Gex was able to save Xtra, and he assures the player that he and Gex will return soon. In the N64 ending, after Gex defeats Rez for the third time, Alfred purchases tickets for Gex and Xtra to go on a relaxing cruise, and Gex allows Alfred to use his remote island for some time off. Gex ignores him and turns the computer off. Just then, Gex's butler, Alfred, tries to warn his master of a world emergency. In the PS1 ending, after defeating Rez for the third time, Gex returns with Xtra to his hotel room, where she tell him about her time in the Media Dimension. Along the way, Gex teams up with his new friends Rex and Cuz. 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. While watching the news on his TV one day, Gex discovers that Agent Xtra (who he met in Gex: Enter The Gecko's backstory), head of the TV Terrorist Defense Unit has been reported as missing.

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