As the game opens following the destruction of SoulStorm Brewery, the Glukkons commercially harvest the froglike Gabbits nearly to extinction, harvesting them for their eggs, to create a caviar-based delicacy called "Gabbiar", and their lungs, needed to replace their own because of their excessive chain-smoking habit. Munch, the last surviving Gabbit, is captured and brought to Vykkers Labs, a floating research fortress, where the Vykkers prepare to convert him into a slave to find animals for them, to allow them more time for their research. After having an electronic device attached to his head for that purpose, Munch finds he can use it to help break free captured Fuzzles, who help him to break free from his own confinement. At the same time, the Mudokon hero Abe is instructed by the "Almighty Raisin", an ancient oracular creature, to find and rescue Munch upon learning of his predicament. Abe reaches the Lab, just as Munch manages to escape via a waste chute, and work together to return to the Raisin.
Upon returning to see him, the Raisin reveals that both need to work together to get back into Vykkers Labs, where Abe can find the eggs off unborn Mudokons that he needs to save. Although not willing to return, Munch learns that the only way to save his species from extinction is to recover the last can of Gabbiar in existence, which is due to be auctioned in the Labs. The duo discover that the only way to infiltrate the Labs and the auction is to assist a lazy Glukkon named Lulu, who desire to achieve a fortune from other Glukkons and elevate himself to the highest rank amongst his species. To assist in this, the duo track down and force various wealthy Glukkons to donate their money to Lulu's accounts, swiftly making him a multi-millionaire. Lulu then heads to Vykkers Labs to bask in his new-found fame and wealth, to which Abe and Munch use the opportunity to break into the Labs. What happens next depends on the overall level of Quarma the player has attained by this point
If the player fails to rescue enough Fuzzles and Mudokon scrubs, attaining less than 50% Quarma, the duo find themselves ambushed by the Fuzzles, who turn on them for not rescuing their kind from the Vykkers. As a result, Abe is killed and has his head displayed as a trophy, while Munch is killed by the Vykkers while extracting his lungs for the Glukkon queen, Lady Margaret. If the player achieves the level of "Black Quarma" (10% Quarma), it's revealed additionally that the Gabbiar has been eaten and the Mudokon eggs have hatched into a new labor force.
If the player has saved a reasonable number of Fuzzles and Mudokons scrubs, attaining 50% Quarma or more, the duo begin working to rescue the eggs of the Mudokons before the auction is to take place, sending them to a transport commandeered by Abe's fellow Mudokons. Eventually, the duo manipulate Lulu to attend the auction and take part in it, with Abe managing to maintain control on him win the auction. In the resulting chaos, the duo rescue the can of Gabbiar and escape from the Labs. As the duo leave across the skies, Abe and Munch watch as Vykkers Labs are destroyed by explosives planted within by the Fuzzles, and witness a second moon in the sky baring the footprint of the Gabbits on its face. If the player achieves the rank of "Angelic Quarma" (90% Quarma), it is revealed that in the aftermath of the destruction of Vykkers Labs, and the liberation of the Mudokon eggs, the industrial economy is thrown into disarray at the hands of Abe and Munch, and Lulu is blamed for it.