Bobby Jenkins lives next door to Leon, a scientist on the verge of discovering a device that can stabilize and control portals connecting the planets within multiple universes. When Leon is transported to another dimension during his experiments, the evil Looger and his cohorts steal the portal technology and use it to break into our world to perfect it. Once here, they are discovered by Bobby who is captured and questioned about Leon's work. Bobby manages to escape and is teleported to their world where the story takes place.
The player can break open cocoons and shells to collect Klokkies and Crystal Gems, which in turn can be used to get new abilities and upgrade existing ones. If the player collects 100 Crystal Gems in the game, an alternate ending will be shown. Lizard Eggs can be gathered to unlock more levels and keep Looger from mutating them into monsters. The game also features a picture gallery; as the player accumulates Crystal Gems, more pictures become available.