Sewer Shark takes place sometime in the future, where environmental destruction has forced most of humanity to live underground. The player takes the role of a rookie pilot in a band of "sewer jockies", whose job is to exterminate dangerous mutated creatures to keep a vast network of sewers clean for the resort area "Solar City", an island paradise ruled by the evil Commissioner Stenchler (Robert Costanzo). The player's co-pilot, Ghost (David Underwood), evaluates the player's performance throughout the game, while a small robot named Catfish scouts ahead and gives directions. The player is later assisted by Falco, a female jockey who believes that there is a hidden route to the surface. Falco is later captured by Stenchler, who threatens to turn her into one of his mindless minions. This plot is thwarted when Ghost and the player reach Solar City.