The game begins with Ratchet and Clank being hired by the company Megacorp to find a small creature that was stolen from the company's labs. Ratchet finds the thief and returns the creature to Megacorp before learning that the creature, called a "protopet", is a dangerous monster which reproduces at amazing speed and that Megacorp is planning to market it to unknowing customers across the Galaxy. The duo must stop the protopet menace and save the galaxy.