Deep Pocket Gecko features two mini-games in which the hero shreds the slopes on a snowboard and hitches a ride with a kangaroo. Also found within each level are fly coins needed to reveal each level's secret remote. Green flies restore one hit paw, purple flies award an extra life, and blue flies activate the gecko's super tail whip power-up. Paw prints can be replenished by eating flies, which come in a variety of colors and may also grant special abilities. Gex earns a remote control each time a task is finished as well as a password, which can be used to resume progress at a later time.Gex begins with five lives, each consisting of four paw prints. To help him meet his goals, the gecko can perform moves such as the tail bounce to reach higher platforms, the run-'n-jump to leap over chasms, and the wall climb to scale specially marked areas.

Gex will need to whack two ice-skating elves, recover the three staffs of Ra, and visit the world's largest mound of poop, among other noble deeds. The goals are to collect hidden remote controls scattered within the game's 11 levels and to defeat arch-nemesis Rez.Each world is broken down into a series of missions, which can be performed in any order.

Each themed world represents a different channel, with players able to switch between Holiday TV, Mystery TV, Tut TV, Western Station, Anime Channel, and the Superhero Show.

Like its predecessor, players control the gecko from a side-scrolling perspective in an adventure spanning six worlds, each of which parodies movies and television. The wisecracking gecko first seen on 3DO makes his second appearance on Game Boy Color with Gex 3: Deep Pocket Gecko.

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